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The 2006 season’s official transaction log: 1,436 trades, signings and releases involving major-league clubs, listed newest first.
| Date | Type | Player | From | To | Details |
|---|---|---|---|---|---|
| Dec 31, 2006 | Signed | Lendy Castillo | — | Philadelphia Phillies | Amateur free agent signing |
| Dec 30, 2006 | Signed as free agent | Dee Brown | — | Arizona Diamondbacks | Free agent signing |
| Dec 30, 2006 | Signed as free agent | D. J. Carrasco | — | Arizona Diamondbacks | Free agent signing |
| Dec 29, 2006 | Signed as free agent | Aaron Boone | — | Florida Marlins | Free agent signing |
| Dec 29, 2006 | Signed as free agent | Barry Zito | — | San Francisco Giants | Free agent signing |
| Dec 28, 2006 | Signed as free agent | Rosman Garcia | — | Baltimore Orioles | Free agent signing |
| Dec 28, 2006 | Signed as free agent | Guillermo Quiroz | — | Texas Rangers | Free agent signing |
| Dec 28, 2006 | Signed as free agent | Mike Wood | — | Texas Rangers | Free agent signing |
| Dec 27, 2006 | Signed as free agent | Chip Ambres | — | New York Mets | Free agent signing |
| Dec 27, 2006 | Signed as free agent | Clint Nageotte | — | New York Mets | Free agent signing |
| Dec 24, 2006 | Signed as free agent | Jeff Suppan | — | Milwaukee Brewers | Free agent signing |
| Dec 23, 2006 | Trade | Nick Masset | Texas Rangers | Chicago White Sox | Trade |
| Dec 23, 2006 | Trade | John Danks | Texas Rangers | Chicago White Sox | Trade |
| Dec 23, 2006 | Trade | Jake Rasner | Texas Rangers | Chicago White Sox | Trade |
| Dec 23, 2006 | Trade | Brandon McCarthy | Chicago White Sox | Texas Rangers | Trade |
| Dec 23, 2006 | Trade | David Paisano | Chicago White Sox | Texas Rangers | Trade |
| Dec 22, 2006 | Signed as free agent | Danny Graves | — | Colorado Rockies | Free agent signing |
| Dec 22, 2006 | Signed as free agent | Runelvys Hernandez | — | Boston Red Sox | Free agent signing |
| Dec 22, 2006 | Signed | Juan Miranda | — | New York Yankees | Amateur free agent signing |
| Dec 22, 2006 | Signed as free agent | Bobby Seay | — | Detroit Tigers | Free agent signing |
| Dec 21, 2006 | Signed as free agent | Rod Barajas | — | Philadelphia Phillies | Free agent signing |
| Dec 21, 2006 | Signed as free agent | Adam Bernero | — | Boston Red Sox | Free agent signing |
| Dec 21, 2006 | Signed as free agent | Joe Dillon | — | Florida Marlins | Free agent signing |
| Dec 21, 2006 | Signed as free agent | Gary Glover | — | Tampa Bay Devil Rays | Free agent signing |
| Dec 21, 2006 | Released | Andy Green | Arizona Diamondbacks | — | Release |
| Dec 21, 2006 | Signed as free agent | Jose Macias | — | Washington Nationals | Free agent signing |
| Dec 21, 2006 | Released | Jerome Williams | Oakland Athletics | — | Release |
| Dec 21, 2006 | Trade | Jeff Conine | Philadelphia Phillies | Cincinnati Reds | Trade |
| Dec 21, 2006 | Trade | Javon Moran | Cincinnati Reds | Philadelphia Phillies | Trade |
| Dec 21, 2006 | Trade | Brad Key | Cincinnati Reds | Philadelphia Phillies | Trade |
| Dec 20, 2006 | Signed as free agent | Zach Day | — | Kansas City Royals | Free agent signing |
| Dec 20, 2006 | Signed as free agent | Einar Diaz | — | Pittsburgh Pirates | Free agent signing |
| Dec 20, 2006 | Signed as free agent | Brandon Duckworth | — | Kansas City Royals | Free agent signing |
| Dec 20, 2006 | Signed as free agent | Robert Fick | — | Washington Nationals | Free agent signing |
| Dec 20, 2006 | Signed as free agent | Marcus Giles | — | San Diego Padres | Free agent signing |
| Dec 20, 2006 | Signed as free agent | Travis Hughes | — | Boston Red Sox | Free agent signing |
| Dec 20, 2006 | Signed as free agent | Curtis Pride | — | Los Angeles Angels of Anaheim | Free agent signing |
| Dec 20, 2006 | Signed as free agent | David Riske | — | Kansas City Royals | Free agent signing |
| Dec 20, 2006 | Signed as free agent | Jared Sandberg | — | Texas Rangers | Free agent signing |
| Dec 20, 2006 | Signed as free agent | Alex Serrano | — | Los Angeles Angels of Anaheim | Free agent signing |
| Dec 20, 2006 | Signed as free agent | Chris Woodward | — | Atlanta Braves | Free agent signing |
| Dec 20, 2006 | Trade | Kevin Gregg | Los Angeles Angels of Anaheim | Florida Marlins | Trade |
| Dec 20, 2006 | Trade | Chris Resop | Florida Marlins | Los Angeles Angels of Anaheim | Trade |
| Dec 19, 2006 | Signed as free agent | Brent Abernathy | — | Philadelphia Phillies | Free agent signing |
| Dec 19, 2006 | Signed as free agent | Eric Gagne | — | Texas Rangers | Free agent signing |
| Dec 19, 2006 | Signed as free agent | Ryan Klesko | — | San Francisco Giants | Free agent signing |
| Dec 19, 2006 | Signed | Masumi Kuwata | — | Pittsburgh Pirates | Amateur free agent signing |
| Dec 19, 2006 | Signed as free agent | Jason Marquis | — | Chicago Cubs | Free agent signing |
| Dec 19, 2006 | Signed as free agent | Jayson Werth | — | Philadelphia Phillies | Free agent signing |
| Dec 18, 2006 | Signed as free agent | Chris Gomez | — | Baltimore Orioles | Free agent signing |
| Dec 18, 2006 | Signed as free agent | Ray King | — | Washington Nationals | Free agent signing |
| Dec 18, 2006 | Signed as free agent | Fernando Lunar | — | Atlanta Braves | Free agent signing |
| Dec 18, 2006 | Signed as free agent | Jason Roach | — | Pittsburgh Pirates | Free agent signing |
| Dec 18, 2006 | Trade | Unnamed | Washington Nationals | Seattle Mariners | $ |
| Dec 18, 2006 | Trade | Jose Vidro | Washington Nationals | Seattle Mariners | Trade |
| Dec 18, 2006 | Trade | Emiliano Fruto | Seattle Mariners | Washington Nationals | Trade |
| Dec 18, 2006 | Trade | Chris Snelling | Seattle Mariners | Washington Nationals | Trade |
| Dec 17, 2006 | Signed as free agent | Toby Hall | — | Chicago White Sox | Free agent signing |
| Dec 16, 2006 | Signed as free agent | Doug Brocail | — | San Diego Padres | Free agent signing |
| Dec 16, 2006 | Signed as free agent | Mike Gallo | — | Colorado Rockies | Free agent signing |
| Dec 16, 2006 | Trade | Andy Sisco | Kansas City Royals | Chicago White Sox | Trade |
| Dec 16, 2006 | Trade | Ross Gload | Chicago White Sox | Kansas City Royals | Trade |
| Dec 15, 2006 | Signed as free agent | Doug Clark | — | Atlanta Braves | Free agent signing |
| Dec 15, 2006 | Signed as free agent | Lance Davis | — | Detroit Tigers | Free agent signing |
| Dec 15, 2006 | Signed as free agent | Jason Karnuth | — | Detroit Tigers | Free agent signing |
| Dec 15, 2006 | Signed as free agent | Ted Lilly | — | Chicago Cubs | Free agent signing |
| Dec 15, 2006 | Signed as free agent | Doug Mirabelli | — | Boston Red Sox | Free agent signing |
| Dec 15, 2006 | Signed as free agent | Chris Oxspring | — | Milwaukee Brewers | Free agent signing |
| Dec 15, 2006 | Signed as free agent | J. C. Romero | — | Boston Red Sox | Free agent signing |
| Dec 15, 2006 | Signed as free agent | Dane Sardinha | — | Detroit Tigers | Free agent signing |
| Dec 15, 2006 | Signed as free agent | Bubba Trammell | — | Baltimore Orioles | Free agent signing |
| Dec 15, 2006 | Signed as free agent | Daryle Ward | — | Chicago Cubs | Free agent signing |
| Dec 15, 2006 | Trade | Brendan Donnelly | Los Angeles Angels of Anaheim | Boston Red Sox | Trade |
| Dec 15, 2006 | Trade | Phil Seibel | Boston Red Sox | Los Angeles Angels of Anaheim | Trade |
| Dec 14, 2006 | Signed as free agent | Miguel Batista | — | Seattle Mariners | Free agent signing |
| Dec 14, 2006 | Signed as free agent | Geronimo Gil | — | Colorado Rockies | Free agent signing |
| Dec 13, 2006 | Signed as free agent | Craig Brazell | — | Kansas City Royals | Free agent signing |
| Dec 13, 2006 | Signed as free agent | Jeff Cirillo | — | Minnesota Twins | Free agent signing |
| Dec 13, 2006 | Signed as free agent | Eric Crozier | — | Boston Red Sox | Free agent signing |
| Dec 13, 2006 | Signed as free agent | Jeff Harris | — | Cleveland Indians | Free agent signing |
| Dec 13, 2006 | Signed | Kelvin Herrera | — | Kansas City Royals | Amateur free agent signing |
| Dec 13, 2006 | Signed as free agent | George Lombard | — | Washington Nationals | Free agent signing |
| Dec 13, 2006 | Signed as free agent | Greg Maddux | — | San Diego Padres | Free agent signing |
| Dec 13, 2006 | Signed as free agent | Gil Meche | — | Kansas City Royals | Free agent signing |
| Dec 13, 2006 | Signed as free agent | Miguel Perez | — | Cincinnati Reds | Free agent signing |
| Dec 13, 2006 | Signed as free agent | Luis Rodriguez | — | Minnesota Twins | Free agent signing |
| Dec 12, 2006 | Signed as free agent | John Barnes | — | Boston Red Sox | Free agent signing |
| Dec 12, 2006 | Signed as free agent | Don Kelly | — | Pittsburgh Pirates | Free agent signing |
| Dec 12, 2006 | Signed as free agent | Kenny Lofton | — | Texas Rangers | Free agent signing |
| Dec 12, 2006 | Signed as free agent | Abraham Nunez | — | Washington Nationals | Free agent signing |
| Dec 12, 2006 | Signed as free agent | Mike Venafro | — | Minnesota Twins | Free agent signing |
| Dec 12, 2006 | Signed as free agent | Brandon Watson | — | Detroit Tigers | Free agent signing |
| Dec 12, 2006 | Trade | Jason Jennings | Colorado Rockies | Houston Astros | Trade |
| Dec 12, 2006 | Trade | Miguel Asencio | Colorado Rockies | Houston Astros | Trade |
| Dec 12, 2006 | Trade | Taylor Buchholz | Houston Astros | Colorado Rockies | Trade |
| Dec 12, 2006 | Trade | Jason Hirsh | Houston Astros | Colorado Rockies | Trade |
| Dec 12, 2006 | Trade | Willy Taveras | Houston Astros | Colorado Rockies | Trade |
| Dec 11, 2006 | Signed as free agent | Cory Bailey | — | Chicago Cubs | Free agent signing |
| Dec 11, 2006 | Signed as free agent | Travis Dawkins | — | Seattle Mariners | Free agent signing |
| Dec 11, 2006 | Signed as free agent | Jeff Farnsworth | — | Philadelphia Phillies | Free agent signing |
| Dec 11, 2006 | Signed as free agent | Eric Junge | — | Cincinnati Reds | Free agent signing |
| Dec 11, 2006 | Signed as free agent | Josh Kroeger | — | Chicago Cubs | Free agent signing |
| Dec 11, 2006 | Signed as free agent | Mike Mahoney | — | Chicago Cubs | Free agent signing |
| Dec 11, 2006 | Signed as free agent | Jose Mesa | — | Detroit Tigers | Free agent signing |
| Dec 11, 2006 | Signed as free agent | Wes Obermueller | — | Florida Marlins | Free agent signing |
| Dec 11, 2006 | Signed as free agent | Darren Oliver | — | Los Angeles Angels of Anaheim | Free agent signing |
| Dec 11, 2006 | Signed as free agent | Jay Payton | — | Baltimore Orioles | Free agent signing |
| Dec 11, 2006 | Signed as free agent | Prentice Redman | — | Seattle Mariners | Free agent signing |
| Dec 11, 2006 | Signed as free agent | Jorge Vasquez | — | New York Mets | Free agent signing |
| Dec 11, 2006 | Signed as free agent | Tyler Walker | — | San Francisco Giants | Free agent signing |
| Dec 10, 2006 | Signed as free agent | Justin Lehr | — | Seattle Mariners | Free agent signing |
| Dec 9, 2006 | Signed as free agent | Willie Harris | — | Atlanta Braves | Free agent signing |
| Dec 9, 2006 | Signed as free agent | Chris Saenz | — | Los Angeles Angels of Anaheim | Free agent signing |
| Dec 8, 2006 | Signed as free agent | Jeff Bailey | — | Boston Red Sox | Free agent signing |
| Dec 8, 2006 | Signed as free agent | John Bale | — | Kansas City Royals | Free agent signing |
| Dec 8, 2006 | Signed as free agent | Jim Brower | — | Pittsburgh Pirates | Free agent signing |
| Dec 8, 2006 | Signed as free agent | Marlon Byrd | — | Texas Rangers | Free agent signing |
| Dec 8, 2006 | Signed as free agent | David Cortes | — | San Francisco Giants | Free agent signing |
| Dec 8, 2006 | Signed as free agent | Octavio Dotel | — | Kansas City Royals | Free agent signing |
| Dec 8, 2006 | Signed as free agent | Luis Gonzalez | — | Los Angeles Dodgers | Free agent signing |
| Dec 8, 2006 | Signed as free agent | Steve Kline | — | San Francisco Giants | Free agent signing |
| Dec 8, 2006 | Signed as free agent | Joe McEwing | — | Boston Red Sox | Free agent signing |
| Dec 8, 2006 | Signed as free agent | Andy Pettitte | — | New York Yankees | Free agent signing |
| Dec 8, 2006 | Signed as free agent | Mike Piazza | — | Oakland Athletics | Free agent signing |
| Dec 8, 2006 | Signed as free agent | Russ Springer | — | St. Louis Cardinals | Free agent signing |
| Dec 8, 2006 | Signed as free agent | Todd Walker | — | San Diego Padres | Free agent signing |
| Dec 7, 2006 | Released | Unnamed | Oakland Athletics | — | Release |
| Dec 7, 2006 | Signed as free agent | Tom Martin | — | Colorado Rockies | Free agent signing |
| Dec 7, 2006 | Signed as free agent | Guillermo Mota | — | New York Mets | Free agent signing |
| Dec 7, 2006 | Released | Aaron Rakers | Baltimore Orioles | — | Release |
| Dec 7, 2006 | Signed as free agent | Matt Stairs | — | Toronto Blue Jays | Free agent signing |
| Dec 7, 2006 | Trade | Kevin Hart | Baltimore Orioles | Chicago Cubs | Trade |
| Dec 7, 2006 | Trade | Horacio Ramirez | Atlanta Braves | Seattle Mariners | Trade |
| Dec 7, 2006 | Trade | Rafael Soriano | Seattle Mariners | Atlanta Braves | Trade |
| Dec 7, 2006 | Trade | Unnamed | Philadelphia Phillies | Baltimore Orioles | $ |
| Dec 7, 2006 | Trade | Adam Donachie | Philadelphia Phillies | Baltimore Orioles | Trade |
| Dec 7, 2006 | Trade | Alfredo Simon | Baltimore Orioles | Philadelphia Phillies | Trade |
| Dec 6, 2006 | Signed as free agent | Paul Bako | — | Baltimore Orioles | Free agent signing |
| Dec 6, 2006 | Signed as free agent | Joe Borowski | — | Cleveland Indians | Free agent signing |
| Dec 6, 2006 | Signed as free agent | Raul Chavez | — | New York Yankees | Free agent signing |
| Dec 6, 2006 | Signed as free agent | David Dellucci | — | Cleveland Indians | Free agent signing |
| Dec 6, 2006 | Released | Juan Dominguez | Oakland Athletics | — | Release |
| Dec 6, 2006 | Signed as free agent | Alan Embree | — | Oakland Athletics | Free agent signing |
| Dec 6, 2006 | Signed as free agent | Mike Lieberthal | — | Los Angeles Dodgers | Free agent signing |
| Dec 6, 2006 | Signed as free agent | Anderson Machado | — | New York Mets | Free agent signing |
| Dec 6, 2006 | Signed as free agent | Bengie Molina | — | San Francisco Giants | Free agent signing |
| Dec 6, 2006 | Signed as free agent | Jason Schmidt | — | Los Angeles Dodgers | Free agent signing |
| Dec 6, 2006 | Trade | Brian Bannister | New York Mets | Kansas City Royals | Trade |
| Dec 6, 2006 | Trade | Ambiorix Burgos | Kansas City Royals | New York Mets | Trade |
| Dec 6, 2006 | Trade | Gavin Floyd | Philadelphia Phillies | Chicago White Sox | Trade |
| Dec 6, 2006 | Trade | Gio Gonzalez | Philadelphia Phillies | Chicago White Sox | Trade |
| Dec 6, 2006 | Trade | Freddy Garcia | Chicago White Sox | Philadelphia Phillies | Trade |
| Dec 6, 2006 | Trade | Freddie Bynum | Chicago Cubs | Baltimore Orioles | Trade |
| Dec 5, 2006 | Signed as free agent | Dewon Brazelton | — | Kansas City Royals | Free agent signing |
| Dec 5, 2006 | Signed as free agent | Jose Cruz | — | San Diego Padres | Free agent signing |
| Dec 5, 2006 | Signed as free agent | LaTroy Hawkins | — | Colorado Rockies | Free agent signing |
| Dec 5, 2006 | Signed as free agent | Julio Lugo | — | Boston Red Sox | Free agent signing |
| Dec 4, 2006 | Signed as free agent | Rich Aurilia | — | San Francisco Giants | Free agent signing |
| Dec 4, 2006 | Signed as free agent | Carmen Cali | — | Minnesota Twins | Free agent signing |
| Dec 4, 2006 | Signed as free agent | Buddy Carlyle | — | Atlanta Braves | Free agent signing |
| Dec 4, 2006 | Signed as free agent | Kane Davis | — | Philadelphia Phillies | Free agent signing |
| Dec 4, 2006 | Signed as free agent | Pedro Feliz | — | San Francisco Giants | Free agent signing |
| Dec 4, 2006 | Signed as free agent | Jose Guillen | — | Seattle Mariners | Free agent signing |
| Dec 4, 2006 | Signed as free agent | Vicente Padilla | — | Texas Rangers | Free agent signing |
| Dec 4, 2006 | Signed as free agent | Kerry Robinson | — | Boston Red Sox | Free agent signing |
| Dec 3, 2006 | Signed as free agent | Tanyon Sturtze | — | Atlanta Braves | Free agent signing |
| Dec 2, 2006 | Signed as free agent | Aaron Fultz | — | Cleveland Indians | Free agent signing |
| Dec 2, 2006 | Signed as free agent | Roberto Hernandez | — | Cleveland Indians | Free agent signing |
| Dec 2, 2006 | Signed as free agent | Kevin Millar | — | Baltimore Orioles | Free agent signing |
| Dec 2, 2006 | Signed as free agent | Dave Roberts | — | San Francisco Giants | Free agent signing |
| Dec 1, 2006 | Signed as free agent | Steve Andrade | — | Tampa Bay Devil Rays | Free agent signing |
| Dec 1, 2006 | Signed as free agent | Edwin Bellorin | — | Colorado Rockies | Free agent signing |
| Dec 1, 2006 | Signed as free agent | Geoff Blum | — | San Diego Padres | Free agent signing |
| Dec 1, 2006 | Signed as free agent | Hee-Seop Choi | — | Tampa Bay Devil Rays | Free agent signing |
| Dec 1, 2006 | Signed as free agent | Roy Corcoran | — | Florida Marlins | Free agent signing |
| Dec 1, 2006 | Signed as free agent | Ray Durham | — | San Francisco Giants | Free agent signing |
| Dec 1, 2006 | Signed as free agent | Tom Glavine | — | New York Mets | Free agent signing |
| Dec 1, 2006 | Signed as free agent | Mike Koplove | — | Florida Marlins | Free agent signing |
| Dec 1, 2006 | Signed as free agent | Ryan Ludwick | — | St. Louis Cardinals | Free agent signing |
| Dec 1, 2006 | Signed as free agent | Dustan Mohr | — | Tampa Bay Devil Rays | Free agent signing |
| Dec 1, 2006 | Signed as free agent | Joe Thurston | — | Washington Nationals | Free agent signing |
| Nov 30, 2006 | Signed as free agent | Hideki Okajima | — | Boston Red Sox | Free agent signing with first major-league team |
| Nov 30, 2006 | Signed as free agent | Terry Tiffee | — | Baltimore Orioles | Free agent signing |
| Nov 30, 2006 | Signed as free agent | Scott Williamson | — | Baltimore Orioles | Free agent signing |
| Nov 29, 2006 | Signed as free agent | Royce Clayton | — | Toronto Blue Jays | Free agent signing |
| Nov 29, 2006 | Signed as free agent | Craig Counsell | — | Milwaukee Brewers | Free agent signing |
| Nov 29, 2006 | Signed as free agent | Enrique Cruz | — | Cincinnati Reds | Free agent signing |
| Nov 29, 2006 | Signed as free agent | Eric DuBose | — | Colorado Rockies | Free agent signing |
| Nov 29, 2006 | Signed as free agent | Mike Edwards | — | Pittsburgh Pirates | Free agent signing |
| Nov 29, 2006 | Signed as free agent | Justin Leone | — | San Francisco Giants | Free agent signing |
| Nov 29, 2006 | Signed as free agent | Jason Shiell | — | Kansas City Royals | Free agent signing |
| Nov 29, 2006 | Signed as free agent | Scott Rice | — | Texas Rangers | Free agent signing |
| Nov 28, 2006 | Signed as free agent | Gary Bennett | — | St. Louis Cardinals | Free agent signing |
| Nov 28, 2006 | Signed as free agent | Chad Bradford | — | Baltimore Orioles | Free agent signing |
| Nov 28, 2006 | Signed as free agent | Adam Kennedy | — | St. Louis Cardinals | Free agent signing |
| Nov 28, 2006 | Signed as free agent | Brandon Larson | — | Washington Nationals | Free agent signing |
| Nov 28, 2006 | Signed as free agent | Eli Marrero | — | St. Louis Cardinals | Free agent signing |
| Nov 28, 2006 | Signed as free agent | Kip Wells | — | St. Louis Cardinals | Free agent signing |
| Nov 28, 2006 | Signed as free agent | Matt White | — | Los Angeles Dodgers | Free agent signing |
| Nov 28, 2006 | Signed as free agent | Randy Wolf | — | Los Angeles Dodgers | Free agent signing |
| Nov 28, 2006 | Signed as free agent | Gregg Zaun | — | Toronto Blue Jays | Free agent signing |
| Nov 27, 2006 | Signed as free agent | Danys Baez | — | Baltimore Orioles | Free agent signing |
| Nov 27, 2006 | Signed as free agent | Adam Eaton | — | Philadelphia Phillies | Free agent signing |
| Nov 27, 2006 | Signed as free agent | Luis Figueroa | — | San Francisco Giants | Free agent signing |
| Nov 27, 2006 | Signed as free agent | Chad Moeller | — | Cincinnati Reds | Free agent signing |
| Nov 27, 2006 | Signed as free agent | Mike Mussina | — | New York Yankees | Free agent signing |
| Nov 27, 2006 | Signed as free agent | Mike Vento | — | Toronto Blue Jays | Free agent signing |
| Nov 26, 2006 | Signed as free agent | Chris Basak | — | New York Yankees | Free agent signing |
| Nov 25, 2006 | Signed as free agent | John Wasdin | — | Pittsburgh Pirates | Free agent signing |
| Nov 25, 2006 | Trade | Doug Davis | Milwaukee Brewers | Arizona Diamondbacks | Trade |
| Nov 25, 2006 | Trade | Dana Eveland | Milwaukee Brewers | Arizona Diamondbacks | Trade |
| Nov 25, 2006 | Trade | Dave Krynzel | Milwaukee Brewers | Arizona Diamondbacks | Trade |
| Nov 25, 2006 | Trade | Johnny Estrada | Arizona Diamondbacks | Milwaukee Brewers | Trade |
| Nov 25, 2006 | Trade | Claudio Vargas | Arizona Diamondbacks | Milwaukee Brewers | Trade |
| Nov 25, 2006 | Trade | Greg Aquino | Arizona Diamondbacks | Milwaukee Brewers | Trade |
| Nov 24, 2006 | Signed as free agent | Alberto Castillo | — | Boston Red Sox | Free agent signing |
| Nov 24, 2006 | Signed as free agent | Jaime Cerda | — | Seattle Mariners | Free agent signing |
| Nov 24, 2006 | Signed as free agent | Eddy Garabito | — | Pittsburgh Pirates | Free agent signing |
| Nov 24, 2006 | Signed as free agent | Carlos Lee | — | Houston Astros | Free agent signing |
| Nov 24, 2006 | Signed as free agent | Mike Rose | — | Cleveland Indians | Free agent signing |
| Nov 24, 2006 | Signed as free agent | Oscar Salazar | — | Baltimore Orioles | Free agent signing |
| Nov 24, 2006 | Signed as free agent | Woody Williams | — | Houston Astros | Free agent signing |
| Nov 23, 2006 | Signed as free agent | Mike Smith | — | St. Louis Cardinals | Free agent signing |
| Nov 22, 2006 | Signed as free agent | Chris Aguila | — | Pittsburgh Pirates | Free agent signing |
| Nov 22, 2006 | Signed as free agent | Chad Bentz | — | Colorado Rockies | Free agent signing |
| Nov 22, 2006 | Signed as free agent | Gary Matthews | — | Los Angeles Angels of Anaheim | Free agent signing |
| Nov 22, 2006 | Signed as free agent | Chris Michalak | — | Washington Nationals | Free agent signing |
| Nov 22, 2006 | Signed as free agent | Juan Pierre | — | Los Angeles Dodgers | Free agent signing |
| Nov 21, 2006 | Signed as free agent | Moises Alou | — | New York Mets | Free agent signing |
| Nov 21, 2006 | Released | Carmen Cali | St. Louis Cardinals | — | Release |
| Nov 21, 2006 | Signed as free agent | Brian Esposito | — | St. Louis Cardinals | Free agent signing |
| Nov 21, 2006 | Signed as free agent | Matt Hensley | — | Los Angeles Angels of Anaheim | Free agent signing |
| Nov 21, 2006 | Signed as free agent | Dave Matranga | — | Texas Rangers | Free agent signing |
| Nov 21, 2006 | Signed as free agent | Bobby Scales | — | Boston Red Sox | Free agent signing |
| Nov 21, 2006 | Signed as free agent | Jamie Walker | — | Baltimore Orioles | Free agent signing |
| Nov 20, 2006 | Signed as free agent | William Bergolla | — | San Francisco Giants | Free agent signing |
| Nov 20, 2006 | Signed as free agent | Ryan Bukvich | — | Chicago White Sox | Free agent signing |
| Nov 20, 2006 | Signed as free agent | Jim Crowell | — | Philadelphia Phillies | Free agent signing |
| Nov 20, 2006 | Signed as free agent | Nomar Garciaparra | — | Los Angeles Dodgers | Free agent signing |
| Nov 20, 2006 | Signed as free agent | Alex Gonzalez | — | Cincinnati Reds | Free agent signing |
| Nov 20, 2006 | Signed as free agent | Mike Kinkade | — | Chicago Cubs | Free agent signing |
| Nov 20, 2006 | Signed as free agent | Carlos Mendez | — | Atlanta Braves | Free agent signing |
| Nov 20, 2006 | Signed as free agent | Neal Musser | — | Kansas City Royals | Free agent signing |
| Nov 20, 2006 | Signed as free agent | Blaine Neal | — | Toronto Blue Jays | Free agent signing |
| Nov 20, 2006 | Signed as free agent | Augie Ojeda | — | Arizona Diamondbacks | Free agent signing |
| Nov 20, 2006 | Signed as free agent | Jailen Peguero | — | Arizona Diamondbacks | Free agent signing |
| Nov 20, 2006 | Signed as free agent | Erasmo Ramirez | — | Oakland Athletics | Free agent signing |
| Nov 20, 2006 | Signed as free agent | Travis Smith | — | Los Angeles Dodgers | Free agent signing |
| Nov 20, 2006 | Signed as free agent | Alfonso Soriano | — | Chicago Cubs | Free agent signing |
| Nov 20, 2006 | Signed as free agent | Mike Stanton | — | Cincinnati Reds | Free agent signing |
| Nov 20, 2006 | Trade | Henry Owens | New York Mets | Florida Marlins | Trade |
| Nov 20, 2006 | Trade | Matt Lindstrom | New York Mets | Florida Marlins | Trade |
| Nov 20, 2006 | Trade | Adam Bostick | Florida Marlins | New York Mets | Trade |
| Nov 20, 2006 | Trade | Jason Vargas | Florida Marlins | New York Mets | Trade |
| Nov 20, 2006 | Signed | Sugar Ray Marimon | — | Kansas City Royals | Amateur free agent signing |
| Nov 19, 2006 | Signed as free agent | Frank Catalanotto | — | Texas Rangers | Free agent signing |
| Nov 19, 2006 | Signed as free agent | Justin Speier | — | Los Angeles Angels of Anaheim | Free agent signing |
| Nov 18, 2006 | Signed as free agent | Scott McClain | — | San Francisco Giants | Free agent signing |
| Nov 18, 2006 | Signed as free agent | Kevin Olsen | — | Oakland Athletics | Free agent signing |
| Nov 18, 2006 | Signed as free agent | Frank Thomas | — | Toronto Blue Jays | Free agent signing |
| Nov 17, 2006 | Signed as free agent | Tim Byrdak | — | Detroit Tigers | Free agent signing |
| Nov 17, 2006 | Signed as free agent | Ron Calloway | — | Philadelphia Phillies | Free agent signing |
| Nov 17, 2006 | Signed as free agent | Alex Cora | — | Boston Red Sox | Free agent signing |
| Nov 17, 2006 | Signed as free agent | Wes Helms | — | Philadelphia Phillies | Free agent signing |
| Nov 17, 2006 | Signed as free agent | Kevin Hooper | — | Detroit Tigers | Free agent signing |
| Nov 17, 2006 | Signed as free agent | Ramon Vazquez | — | Texas Rangers | Free agent signing |
| Nov 17, 2006 | Signed | Andre Rienzo | — | Chicago White Sox | Amateur free agent signing |
| Nov 16, 2006 | Signed as free agent | Jamie Burke | — | Seattle Mariners | Free agent signing |
| Nov 16, 2006 | Signed as free agent | Sean Casey | — | Detroit Tigers | Free agent signing |
| Nov 16, 2006 | Signed as free agent | Damion Easley | — | New York Mets | Free agent signing |
| Nov 16, 2006 | Signed as free agent | Ken Huckaby | — | Los Angeles Dodgers | Free agent signing |
| Nov 16, 2006 | Signed as free agent | Randy Keisler | — | St. Louis Cardinals | Free agent signing |
| Nov 16, 2006 | Signed as free agent | Sandy Martinez | — | Los Angeles Dodgers | Free agent signing |
| Nov 16, 2006 | Signed as free agent | Scott Spiezio | — | St. Louis Cardinals | Free agent signing |
| Nov 16, 2006 | Signed as free agent | Ernie Young | — | Chicago White Sox | Free agent signing |
| Nov 16, 2006 | Trade | Neal Cotts | Chicago White Sox | Chicago Cubs | Trade |
| Nov 16, 2006 | Trade | David Aardsma | Chicago Cubs | Chicago White Sox | Trade |
| Nov 16, 2006 | Trade | Carlos Vasquez | Chicago Cubs | Chicago White Sox | Trade |
| Nov 15, 2006 | Signed as free agent | Henry Blanco | — | Chicago Cubs | Free agent signing |
| Nov 15, 2006 | Signed as free agent | Scott Dunn | — | Oakland Athletics | Free agent signing |
| Nov 15, 2006 | Signed as free agent | John Gall | — | Florida Marlins | Free agent signing |
| Nov 15, 2006 | Signed as free agent | Jesse Garcia | — | Houston Astros | Free agent signing |
| Nov 15, 2006 | Signed as free agent | Franklyn German | — | Texas Rangers | Free agent signing |
| Nov 15, 2006 | Signed as free agent | Adam Greenberg | — | Kansas City Royals | Free agent signing |
| Nov 15, 2006 | Signed as free agent | Jon Leicester | — | Baltimore Orioles | Free agent signing |
| Nov 15, 2006 | Signed as free agent | Colby Lewis | — | Washington Nationals | Free agent signing |
| Nov 15, 2006 | Trade | Jon Adkins | San Diego Padres | New York Mets | Trade |
| Nov 15, 2006 | Trade | Ben Johnson | San Diego Padres | New York Mets | Trade |
| Nov 15, 2006 | Trade | Heath Bell | New York Mets | San Diego Padres | Trade |
| Nov 15, 2006 | Trade | Royce Ring | New York Mets | San Diego Padres | Trade |
| Nov 14, 2006 | Signed as free agent | Mark DeRosa | — | Chicago Cubs | Free agent signing |
| Nov 14, 2006 | Signed as free agent | Orlando Hernandez | — | New York Mets | Free agent signing |
| Nov 14, 2006 | Signed as free agent | Luis Montanez | — | Baltimore Orioles | Free agent signing |
| Nov 14, 2006 | Signed as free agent | Steve Torrealba | — | Detroit Tigers | Free agent signing |
| Nov 13, 2006 | Signed as free agent | Scott Atchison | — | San Francisco Giants | Free agent signing |
| Nov 13, 2006 | Signed as free agent | Jeff Bennett | — | Atlanta Braves | Free agent signing |
| Nov 13, 2006 | Signed as free agent | Brian Bowles | — | San Francisco Giants | Free agent signing |
| Nov 13, 2006 | Signed as free agent | Cesar Crespo | — | Baltimore Orioles | Free agent signing |
| Nov 13, 2006 | Signed as free agent | Vic Darensbourg | — | Detroit Tigers | Free agent signing |
| Nov 13, 2006 | Signed as free agent | Mike Hessman | — | Detroit Tigers | Free agent signing |
| Nov 13, 2006 | Signed as free agent | Paul Hoover | — | Florida Marlins | Free agent signing |
| Nov 13, 2006 | Signed as free agent | J. R. House | — | Baltimore Orioles | Free agent signing |
| Nov 13, 2006 | Signed as free agent | Kazuo Matsui | — | Colorado Rockies | Free agent signing |
| Nov 13, 2006 | Signed as free agent | Brian Myrow | — | San Diego Padres | Free agent signing |
| Nov 13, 2006 | Signed as free agent | Matt Roney | — | Toronto Blue Jays | Free agent signing |
| Nov 13, 2006 | Signed as free agent | John Webb | — | Chicago Cubs | Free agent signing |
| Nov 12, 2006 | Signed as free agent | Juan Brito | — | Washington Nationals | Free agent signing |
| Nov 12, 2006 | Signed as free agent | Ben Howard | — | Chicago Cubs | Free agent signing |
| Nov 12, 2006 | Signed as free agent | Aramis Ramirez | — | Chicago Cubs | Free agent signing |
| Nov 12, 2006 | Signed as free agent | Jason Smith | — | Chicago Cubs | Free agent signing |
| Nov 12, 2006 | Signed as free agent | Kerry Wood | — | Chicago Cubs | Free agent signing |
| Nov 12, 2006 | Trade | Unnamed | New York Yankees | Baltimore Orioles | $ |
| Nov 12, 2006 | Trade | Jaret Wright | New York Yankees | Baltimore Orioles | Trade |
| Nov 12, 2006 | Trade | Chris Britton | Baltimore Orioles | New York Yankees | Trade |
| Nov 11, 2006 | Signed as free agent | Dan Giese | — | San Francisco Giants | Free agent signing |
| Nov 11, 2006 | Signed as free agent | Mike Johnston | — | San Diego Padres | Free agent signing |
| Nov 11, 2006 | Signed as free agent | Steve Watkins | — | San Diego Padres | Free agent signing |
| Nov 10, 2006 | Signed as free agent | Craig Biggio | — | Houston Astros | Free agent signing |
| Nov 10, 2006 | Signed as free agent | Bubba Crosby | — | Cincinnati Reds | Free agent signing |
| Nov 10, 2006 | Signed as free agent | Jeff Duncan | — | Toronto Blue Jays | Free agent signing |
| Nov 10, 2006 | Signed as free agent | John Ennis | — | Philadelphia Phillies | Free agent signing |
| Nov 10, 2006 | Signed as free agent | Geremi Gonzalez | — | Toronto Blue Jays | Free agent signing |
| Nov 10, 2006 | Signed as free agent | Koyie Hill | — | Chicago Cubs | Free agent signing |
| Nov 10, 2006 | Signed as free agent | Luis Jimenez | — | Boston Red Sox | Free agent signing |
| Nov 10, 2006 | Signed as free agent | Mark Johnson | — | Arizona Diamondbacks | Free agent signing |
| Nov 10, 2006 | Signed as free agent | Bobby Keppel | — | Colorado Rockies | Free agent signing |
| Nov 10, 2006 | Signed as free agent | Chad Mottola | — | Toronto Blue Jays | Free agent signing |
| Nov 10, 2006 | Signed as free agent | Josh Phelps | — | Baltimore Orioles | Free agent signing |
| Nov 10, 2006 | Signed as free agent | Tony Torcato | — | Seattle Mariners | Free agent signing |
| Nov 10, 2006 | Signed as free agent | Raul Valdes | — | New York Mets | Free agent signing |
| Nov 10, 2006 | Signed as free agent | Jorge Velandia | — | Tampa Bay Devil Rays | Free agent signing |
| Nov 10, 2006 | Trade | Gary Sheffield | New York Yankees | Detroit Tigers | Trade |
| Nov 10, 2006 | Trade | Anthony Claggett | Detroit Tigers | New York Yankees | Trade |
| Nov 10, 2006 | Trade | Humberto Sanchez | Detroit Tigers | New York Yankees | Trade |
| Nov 10, 2006 | Trade | Kevin Whelan | Detroit Tigers | New York Yankees | Trade |
| Nov 9, 2006 | Signed as free agent | Jason Anderson | — | Chicago Cubs | Free agent signing |
| Nov 9, 2006 | Signed as free agent | Ronald Belisario | — | Pittsburgh Pirates | Free agent signing |
| Nov 9, 2006 | Signed as free agent | Mike Cervenak | — | Baltimore Orioles | Free agent signing |
| Nov 9, 2006 | Signed as free agent | Steve Colyer | — | Atlanta Braves | Free agent signing |
| Nov 9, 2006 | Signed as free agent | Nate Field | — | Florida Marlins | Free agent signing |
| Nov 9, 2006 | Signed as free agent | Lee Gardner | — | Florida Marlins | Free agent signing |
| Nov 9, 2006 | Signed as free agent | Wade Miller | — | Chicago Cubs | Free agent signing |
| Nov 9, 2006 | Released | Tyler Walker | Tampa Bay Devil Rays | — | Release |
| Nov 9, 2006 | Signed as free agent | Bill White | — | Washington Nationals | Free agent signing |
| Nov 9, 2006 | Signed as free agent | Jason Wood | — | Florida Marlins | Free agent signing |
| Nov 8, 2006 | Signed as free agent | Jeff Bajenaru | — | Arizona Diamondbacks | Free agent signing |
| Nov 8, 2006 | Signed as free agent | Frank Brooks | — | San Diego Padres | Free agent signing |
| Nov 8, 2006 | Signed as free agent | Jesus Colome | — | Washington Nationals | Free agent signing |
| Nov 8, 2006 | Signed as free agent | Matt Kata | — | Texas Rangers | Free agent signing |
| Nov 8, 2006 | Signed as free agent | Graham Koonce | — | Kansas City Royals | Free agent signing |
| Nov 8, 2006 | Signed as free agent | Josh Wilson | — | Washington Nationals | Free agent signing |
| Nov 8, 2006 | Trade | Josh Barfield | San Diego Padres | Cleveland Indians | Trade |
| Nov 8, 2006 | Trade | Andrew Brown | Cleveland Indians | San Diego Padres | Trade |
| Nov 8, 2006 | Trade | Kevin Kouzmanoff | Cleveland Indians | San Diego Padres | Trade |
| Nov 7, 2006 | Signed as free agent | J. J. Furmaniak | — | Oakland Athletics | Free agent signing |
| Nov 7, 2006 | Signed as free agent | Ramon Martinez | — | Los Angeles Dodgers | Free agent signing |
| Nov 7, 2006 | Signed as free agent | Corky Miller | — | Atlanta Braves | Free agent signing |
| Nov 7, 2006 | Signed as free agent | Lino Urdaneta | — | New York Mets | Free agent signing |
| Nov 6, 2006 | Signed as free agent | Danny Ardoin | — | Washington Nationals | Free agent signing |
| Nov 6, 2006 | Signed as free agent | Rob Bell | — | Baltimore Orioles | Free agent signing |
| Nov 6, 2006 | Signed as free agent | Nate Bland | — | Chicago Cubs | Free agent signing |
| Nov 6, 2006 | Signed as free agent | Felix Diaz | — | Washington Nationals | Free agent signing |
| Nov 6, 2006 | Signed as free agent | Cory Doyne | — | Baltimore Orioles | Free agent signing |
| Nov 6, 2006 | Signed as free agent | Josh Hall | — | Washington Nationals | Free agent signing |
| Nov 6, 2006 | Signed as free agent | Joel Hanrahan | — | Washington Nationals | Free agent signing |
| Nov 6, 2006 | Signed as free agent | Alejandro Machado | — | Washington Nationals | Free agent signing |
| Nov 6, 2006 | Signed as free agent | Darnell McDonald | — | Washington Nationals | Free agent signing |
| Nov 6, 2006 | Signed as free agent | Tim Redding | — | Washington Nationals | Free agent signing |
| Nov 6, 2006 | Signed as free agent | Adam Shabala | — | San Diego Padres | Free agent signing |
| Nov 4, 2006 | Signed as free agent | Steve Green | — | Baltimore Orioles | Free agent signing |
| Nov 4, 2006 | Signed as free agent | Michael Restovich | — | Washington Nationals | Free agent signing |
| Nov 3, 2006 | Signed as free agent | Angel Chavez | — | New York Yankees | Free agent signing |
| Nov 3, 2006 | Signed as free agent | Alfredo Simon | — | Texas Rangers | Free agent signing |
| Nov 2, 2006 | Signed as free agent | Ben Kozlowski | — | New York Yankees | Free agent signing |
| Nov 2, 2006 | Signed as free agent | Eider Torres | — | Baltimore Orioles | Free agent signing |
| Nov 2, 2006 | Signed as free agent | Brian Wolfe | — | Toronto Blue Jays | Free agent signing |
| Nov 1, 2006 | Signed | Pedro Hernandez | — | San Diego Padres | Amateur free agent signing |
| Nov 1, 2006 | Signed as free agent | Scott Patterson | — | New York Yankees | Free agent signing |
| Nov 1, 2006 | Signed as free agent | Allan Simpson | — | Pittsburgh Pirates | Free agent signing |
| Nov 1, 2006 | Signed as free agent | Pedro Swann | — | Philadelphia Phillies | Free agent signing |
| Nov 1, 2006 | Signed | Jose De Paula | — | San Diego Padres | Amateur free agent signing |
| Oct 31, 2006 | Released | Jeff Harris | Seattle Mariners | — | Release |
| Oct 31, 2006 | Signed as free agent | Jean Machi | — | Toronto Blue Jays | Free agent signing |
| Oct 31, 2006 | Signed as free agent | Mike Ryan | — | Pittsburgh Pirates | Free agent signing |
| Oct 31, 2006 | Signed as free agent | Todd Sears | — | Florida Marlins | Free agent signing |
| Oct 31, 2006 | Signed as free agent | Zach Sorensen | — | Florida Marlins | Free agent signing |
| Oct 30, 2006 | Signed as free agent | Ryan Jorgensen | — | Cincinnati Reds | Free agent signing |
| Oct 30, 2006 | Signed as free agent | Eddy Rodriguez | — | Florida Marlins | Free agent signing |
| Oct 30, 2006 | Signed as free agent | Rich Thompson | — | Arizona Diamondbacks | Free agent signing |
| Oct 30, 2006 | Signed as free agent | Ed Yarnall | — | Kansas City Royals | Free agent signing |
| Oct 28, 2006 | Signed as free agent | Jermaine Van Buren | — | Washington Nationals | Free agent signing |
| Oct 28, 2006 | Signed as free agent | Chris Waters | — | Baltimore Orioles | Free agent signing |
| Oct 27, 2006 | Signed as free agent | Wayne Franklin | — | Kansas City Royals | Free agent signing |
| Oct 27, 2006 | Signed as free agent | Dewayne Wise | — | Cincinnati Reds | Free agent signing |
| Oct 26, 2006 | Signed as free agent | Scott Strickland | — | San Diego Padres | Free agent signing |
| Oct 26, 2006 | Signed as free agent | Cody Clark | — | Kansas City Royals | Free agent signing |
| Oct 25, 2006 | Signed | Starlin Castro | — | Chicago Cubs | Amateur free agent signing |
| Oct 25, 2006 | Signed as free agent | Ivan Ochoa | — | San Francisco Giants | Free agent signing |
| Oct 23, 2006 | Released | D'Angelo Jimenez | Oakland Athletics | — | Release |
| Oct 23, 2006 | Released | Curtis Pride | Los Angeles Angels of Anaheim | — | Release |
| Oct 22, 2006 | Signed as free agent | Kevin Barker | — | Toronto Blue Jays | Free agent signing |
| Oct 22, 2006 | Signed as free agent | Chris George | — | Florida Marlins | Free agent signing |
| Oct 22, 2006 | Signed as free agent | Rico Washington | — | St. Louis Cardinals | Free agent signing |
| Oct 17, 2006 | Signed | Henderson Alvarez | — | Toronto Blue Jays | Amateur free agent signing |
| Oct 17, 2006 | Signed | Jesus Montero | — | New York Yankees | Amateur free agent signing |
| Oct 17, 2006 | Signed as free agent | Chris Spurling | — | Milwaukee Brewers | Free agent signing |
| Oct 16, 2006 | Released | Kevin Witt | Tampa Bay Devil Rays | — | Release |
| Oct 15, 2006 | Released | Jared Sandberg | Cleveland Indians | — | Release |
| Oct 15, 2006 | Signed as free agent | Chad Santos | — | San Francisco Giants | Free agent signing |
| Oct 13, 2006 | Signed as free agent | Melvin Dorta | — | Washington Nationals | Free agent signing |
| Oct 13, 2006 | Trade | Trevor Lawhorn | Cincinnati Reds | Toronto Blue Jays | Trade |
| Oct 13, 2006 | Trade | Jerry Gil | Arizona Diamondbacks | Cincinnati Reds | Trade |
| Oct 13, 2006 | Trade | Abe Woody | Cincinnati Reds | Arizona Diamondbacks | Trade |
| Oct 12, 2006 | Released | Mark Bellhorn | San Diego Padres | — | Release |
| Oct 12, 2006 | Released | Geremi Gonzalez | Milwaukee Brewers | — | Release |
| Oct 11, 2006 | Released | Julio Santana | Philadelphia Phillies | — | Release |
| Oct 11, 2006 | Signed | Mayckol Guaipe | — | Seattle Mariners | Amateur free agent signing |
| Oct 10, 2006 | Released | John Foster | Atlanta Braves | — | Release |
| Oct 10, 2006 | Signed | Salvador Perez | — | Kansas City Royals | Amateur free agent signing |
| Oct 10, 2006 | Released | Scott Sauerbeck | Oakland Athletics | — | Release |
| Oct 3, 2006 | Released | Zach Day | Washington Nationals | — | Release |
| Oct 3, 2006 | Released | Ryan Drese | Washington Nationals | — | Release |
| Oct 3, 2006 | Released | Brian Lawrence | Washington Nationals | — | Release |
| Oct 3, 2006 | Trade | Adam Stern | Boston Red Sox | Baltimore Orioles | Trade |
| Oct 1, 2006 | Released | Pedro Astacio | Washington Nationals | — | Release |
| Oct 1, 2006 | Released | Joey Eischen | Washington Nationals | — | Release |
| Oct 1, 2006 | Released | Felix Rodriguez | Washington Nationals | — | Release |
| Sep 23, 2006 | Signed | Carlos Triunfel | — | Seattle Mariners | Amateur free agent signing |
| Sep 21, 2006 | Released | Brian Boehringer | Detroit Tigers | — | Release |
| Sep 15, 2006 | Trade | Dale Thayer | San Diego Padres | Tampa Bay Devil Rays | Trade |
| Sep 13, 2006 | Released | Ben Davis | New York Yankees | — | Release |
| Sep 10, 2006 | Released | Travis Lee | Tampa Bay Devil Rays | — | Release |
| Sep 8, 2006 | Released | Scott Chiasson | Cincinnati Reds | — | Release |
| Sep 8, 2006 | Released | Javy Lopez | Boston Red Sox | — | Release |
| Sep 7, 2006 | Signed as free agent | Robert Coello | — | Los Angeles Angels of Anaheim | Free agent signing |
| Sep 7, 2006 | Released | Pat Mahomes | Kansas City Royals | — | Release |
| Sep 6, 2006 | Released | Dmitri Young | Detroit Tigers | — | Release |
| Sep 5, 2006 | Trade | George Kottaras | San Diego Padres | Boston Red Sox | Trade |
| Sep 5, 2006 | Trade | Adam Harben | Minnesota Twins | Chicago Cubs | Trade |
| Sep 1, 2006 | Released | Bobby Madritsch | Kansas City Royals | — | Release |
| Aug 31, 2006 | Released | Tom Gregorio | Texas Rangers | — | Release |
| Aug 31, 2006 | Signed as free agent | Jason Johnson | — | Cincinnati Reds | Free agent signing |
| Aug 31, 2006 | Signed as free agent | Rudy Seanez | — | San Diego Padres | Free agent signing |
| Aug 31, 2006 | Trade | Daryle Ward | Washington Nationals | Atlanta Braves | Trade |
| Aug 31, 2006 | Trade | Luis Atilano | Atlanta Braves | Washington Nationals | Trade |
| Aug 31, 2006 | Trade | Marlon Anderson | Washington Nationals | Los Angeles Dodgers | Trade |
| Aug 31, 2006 | Trade | Jhonny Nunez | Los Angeles Dodgers | Washington Nationals | Trade |
| Aug 31, 2006 | Trade | David Wells | Boston Red Sox | San Diego Padres | Trade |
| Aug 31, 2006 | Trade | Unnamed | Chicago Cubs | Minnesota Twins | $ |
| Aug 31, 2006 | Trade | Phil Nevin | Chicago Cubs | Minnesota Twins | Trade |
| Aug 30, 2006 | Trade | Angel Chavez | Philadelphia Phillies | Baltimore Orioles | Trade |
| Aug 30, 2006 | Trade | Victor Diaz | New York Mets | Texas Rangers | Trade |
| Aug 30, 2006 | Trade | Mike Nickeas | Texas Rangers | New York Mets | Trade |
| Aug 29, 2006 | Signed as free agent | T. J. Mathews | — | Boston Red Sox | Free agent signing |
| Aug 29, 2006 | Released | Donovan Osborne | Kansas City Royals | — | Release |
| Aug 28, 2006 | Released | Jason Johnson | Boston Red Sox | — | Release |
| Aug 28, 2006 | Released | Jose Morban | Seattle Mariners | — | Release |
| Aug 28, 2006 | Trade | Unnamed | Boston Red Sox | Cincinnati Reds | $ |
| Aug 28, 2006 | Trade | Tim Bausher | Boston Red Sox | Cincinnati Reds | Trade |
| Aug 28, 2006 | Trade | Mike Burns | Cincinnati Reds | Boston Red Sox | Trade |
| Aug 28, 2006 | Signed | Joe Ortiz | — | Texas Rangers | Amateur free agent signing |
| Aug 27, 2006 | Trade | Jeff Conine | Baltimore Orioles | Philadelphia Phillies | Trade |
| Aug 26, 2006 | Released | Carlos Almanzar | Atlanta Braves | — | Release |
| Aug 26, 2006 | Released | Tony Alvarez | Baltimore Orioles | — | Release |
| Aug 25, 2006 | Released | Damian Jackson | Washington Nationals | — | Release |
| Aug 24, 2006 | Signed as free agent | Kelly Stinnett | — | New York Mets | Free agent signing |
| Aug 24, 2006 | Trade | Shawn Nottingham | Seattle Mariners | Cleveland Indians | Trade |
| Aug 24, 2006 | Trade | Russell Branyan | Tampa Bay Devil Rays | San Diego Padres | Trade |
| Aug 24, 2006 | Trade | Evan Meek | San Diego Padres | Tampa Bay Devil Rays | Trade |
| Aug 23, 2006 | Signed as free agent | Mike Garcia | — | Chicago Cubs | Free agent signing |
| Aug 23, 2006 | Released | Sidney Ponson | New York Yankees | — | Release |
| Aug 23, 2006 | Signed as free agent | Jose Vizcaino | — | St. Louis Cardinals | Free agent signing |
| Aug 22, 2006 | Signed | Cole De Vries | — | Minnesota Twins | Amateur free agent signing |
| Aug 22, 2006 | Trade | Unnamed | Arizona Diamondbacks | New York Mets | $ |
| Aug 22, 2006 | Trade | Shawn Green | Arizona Diamondbacks | New York Mets | Trade |
| Aug 22, 2006 | Trade | Evan MacLane | New York Mets | Arizona Diamondbacks | Trade |
| Aug 21, 2006 | Released | Franklyn German | Florida Marlins | — | Release |
| Aug 21, 2006 | Signed | Juan Nicasio | — | Colorado Rockies | Amateur free agent signing |
| Aug 21, 2006 | Signed | Diego Moreno | — | Pittsburgh Pirates | Amateur free agent signing |
| Aug 20, 2006 | Trade | Neifi Perez | Chicago Cubs | Detroit Tigers | Trade |
| Aug 20, 2006 | Trade | Chris Robinson | Detroit Tigers | Chicago Cubs | Trade |
| Aug 19, 2006 | Released | Rudy Seanez | Boston Red Sox | — | Release |
| Aug 19, 2006 | Trade | Jamie Moyer | Seattle Mariners | Philadelphia Phillies | Trade |
| Aug 19, 2006 | Trade | Andrew Baldwin | Philadelphia Phillies | Seattle Mariners | Trade |
| Aug 19, 2006 | Trade | Andy Barb | Philadelphia Phillies | Seattle Mariners | Trade |
| Aug 18, 2006 | Released | Jose Vizcaino | San Francisco Giants | — | Release |
| Aug 18, 2006 | Signed as free agent | Preston Wilson | — | St. Louis Cardinals | Free agent signing |
| Aug 17, 2006 | Signed as free agent | Eric Knott | — | Texas Rangers | Free agent signing |
| Aug 17, 2006 | Signed as free agent | Frank Menechino | — | New York Yankees | Free agent signing |
| Aug 17, 2006 | Signed as free agent | Carlos Peña | — | Boston Red Sox | Free agent signing |
| Aug 17, 2006 | Released | Roberto Petagine | Seattle Mariners | — | Release |
| Aug 16, 2006 | Released | Chad Harville | Tampa Bay Devil Rays | — | Release |
| Aug 16, 2006 | Released | Pedro Liriano | San Francisco Giants | — | Release |
| Aug 16, 2006 | Released | Carlos Peña | New York Yankees | — | Release |
| Aug 16, 2006 | Trade | Scott Schoeneweis | Toronto Blue Jays | Cincinnati Reds | Trade |
| Aug 14, 2006 | Released | Sean Burroughs | Tampa Bay Devil Rays | — | Release |
| Aug 14, 2006 | Signed as free agent | Vinny Castilla | — | Colorado Rockies | Free agent signing |
| Aug 14, 2006 | Signed as free agent | Bryan Corey | — | Boston Red Sox | Free agent signing |
| Aug 12, 2006 | Released | Adrian Brown | Texas Rangers | — | Release |
| Aug 12, 2006 | Released | Preston Wilson | Houston Astros | — | Release |
| Aug 11, 2006 | Signed | John Axford | — | New York Yankees | Amateur free agent signing |
| Aug 11, 2006 | Released | Jaime Cerda | Colorado Rockies | — | Release |
| Aug 11, 2006 | Signed as free agent | Luther Hackman | — | Milwaukee Brewers | Free agent signing |
| Aug 11, 2006 | Signed as free agent | Mac Suzuki | — | Chicago Cubs | Free agent signing |
| Aug 11, 2006 | Signed as free agent | Eric Young | — | Texas Rangers | Free agent signing |
| Aug 10, 2006 | Signed | Maikel Cleto | — | New York Mets | Amateur free agent signing |
| Aug 10, 2006 | Signed | Brandon Dickson | — | St. Louis Cardinals | Amateur free agent signing |
| Aug 10, 2006 | Released | Luis Matos | Washington Nationals | — | Release |
| Aug 9, 2006 | Released | Eli Marrero | New York Mets | — | Release |
| Aug 9, 2006 | Trade | Zac Stott | Cincinnati Reds | Philadelphia Phillies | Trade |
| Aug 8, 2006 | Released | Brian Daubach | St. Louis Cardinals | — | Release |
| Aug 8, 2006 | Signed as free agent | David Lee | — | Boston Red Sox | Free agent signing |
| Aug 8, 2006 | Released | Orber Moreno | St. Louis Cardinals | — | Release |
| Aug 7, 2006 | Trade | Unnamed | Washington Nationals | Arizona Diamondbacks | $ |
| Aug 7, 2006 | Trade | Livan Hernandez | Washington Nationals | Arizona Diamondbacks | Trade |
| Aug 7, 2006 | Trade | Garrett Mock | Arizona Diamondbacks | Washington Nationals | Trade |
| Aug 7, 2006 | Trade | Matt Chico | Arizona Diamondbacks | Washington Nationals | Trade |
| Aug 7, 2006 | Trade | Unnamed | Philadelphia Phillies | Cincinnati Reds | $ |
| Aug 7, 2006 | Trade | Ryan Franklin | Philadelphia Phillies | Cincinnati Reds | Trade |
| Aug 5, 2006 | Released | Erubiel Durazo | Minnesota Twins | — | Release |
| Aug 5, 2006 | Released | Clint Sodowsky | Atlanta Braves | — | Release |
| Aug 4, 2006 | Signed as free agent | Pat Mahomes | — | Kansas City Royals | Free agent signing |
| Aug 4, 2006 | Signed as free agent | Tike Redman | — | Houston Astros | Free agent signing |
| Aug 4, 2006 | Signed as free agent | Randall Simon | — | Texas Rangers | Free agent signing |
| Aug 4, 2006 | Signed as free agent | Jorge Toca | — | St. Louis Cardinals | Free agent signing |
| Aug 4, 2006 | Signed as free agent | Chris Widger | — | Baltimore Orioles | Free agent signing |
| Aug 4, 2006 | Trade | Unnamed | Boston Red Sox | Baltimore Orioles | $ |
| Aug 4, 2006 | Trade | Javy Lopez | Baltimore Orioles | Boston Red Sox | Trade |
| Aug 3, 2006 | Released | Jason Conti | St. Louis Cardinals | — | Release |
| Aug 3, 2006 | Released | Steve Lomasney | Minnesota Twins | — | Release |
| Aug 3, 2006 | Signed as free agent | Brian Myrow | — | Boston Red Sox | Free agent signing |
| Aug 2, 2006 | Released | David Lee | Florida Marlins | — | Release |
| Aug 1, 2006 | Released | Jose Cruz | Los Angeles Dodgers | — | Release |
| Aug 1, 2006 | Released | Steve Kent | Houston Astros | — | Release |
| Aug 1, 2006 | Released | Franklin Nunez | Atlanta Braves | — | Release |
| Aug 1, 2006 | Released | Eric Young | San Diego Padres | — | Release |
| Aug 1, 2006 | Trade | Matt Blank | Florida Marlins | San Diego Padres | Trade |
| Aug 1, 2006 | Trade | Jim Brower | San Diego Padres | Florida Marlins | Trade |
| Aug 1, 2006 | Signed | Mauricio Robles | — | Detroit Tigers | Amateur free agent signing |
| Jul 31, 2006 | Released | Jeriome Robertson | New York Mets | — | Release |
| Jul 31, 2006 | Released | John Wasdin | Texas Rangers | — | Release |
| Jul 31, 2006 | Released | Enrique Wilson | Boston Red Sox | — | Release |
| Jul 31, 2006 | Trade | Matt Stairs | Kansas City Royals | Texas Rangers | Trade |
| Jul 31, 2006 | Trade | Jose Diaz | Texas Rangers | Kansas City Royals | Trade |
| Jul 31, 2006 | Trade | Kip Wells | Pittsburgh Pirates | Texas Rangers | Trade |
| Jul 31, 2006 | Trade | Jesse Chavez | Texas Rangers | Pittsburgh Pirates | Trade |
| Jul 31, 2006 | Trade | Julio Lugo | Tampa Bay Devil Rays | Los Angeles Dodgers | Trade |
| Jul 31, 2006 | Trade | Joel Guzman | Los Angeles Dodgers | Tampa Bay Devil Rays | Trade |
| Jul 31, 2006 | Trade | Sergio Pedroza | Los Angeles Dodgers | Tampa Bay Devil Rays | Trade |
| Jul 31, 2006 | Trade | Jorge Sosa | Atlanta Braves | St. Louis Cardinals | Trade |
| Jul 31, 2006 | Trade | Rich Scalamandre | St. Louis Cardinals | Atlanta Braves | Trade |
| Jul 31, 2006 | Trade | Todd Walker | Chicago Cubs | San Diego Padres | Trade |
| Jul 31, 2006 | Trade | Jose Ceda | San Diego Padres | Chicago Cubs | Trade |
| Jul 31, 2006 | Trade | Sean Casey | Pittsburgh Pirates | Detroit Tigers | Trade |
| Jul 31, 2006 | Trade | Brian Rogers | Detroit Tigers | Pittsburgh Pirates | Trade |
| Jul 31, 2006 | Trade | Xavier Nady | New York Mets | Pittsburgh Pirates | Trade |
| Jul 31, 2006 | Trade | Roberto Hernandez | Pittsburgh Pirates | New York Mets | Trade |
| Jul 31, 2006 | Trade | Oliver Perez | Pittsburgh Pirates | New York Mets | Trade |
| Jul 31, 2006 | Trade | Shawn Chacon | New York Yankees | Pittsburgh Pirates | Trade |
| Jul 31, 2006 | Trade | Craig Wilson | Pittsburgh Pirates | New York Yankees | Trade |
| Jul 31, 2006 | Trade | Rheal Cormier | Philadelphia Phillies | Cincinnati Reds | Trade |
| Jul 31, 2006 | Trade | Justin Germano | Cincinnati Reds | Philadelphia Phillies | Trade |
| Jul 31, 2006 | Trade | Kyle Lohse | Minnesota Twins | Cincinnati Reds | Trade |
| Jul 31, 2006 | Trade | Zach Ward | Cincinnati Reds | Minnesota Twins | Trade |
| Jul 31, 2006 | Trade | Greg Maddux | Chicago Cubs | Los Angeles Dodgers | Trade |
| Jul 31, 2006 | Trade | Cesar Izturis | Los Angeles Dodgers | Chicago Cubs | Trade |
| Jul 31, 2006 | Trade | Ryan Shealy | Colorado Rockies | Kansas City Royals | Trade |
| Jul 31, 2006 | Trade | Scott Dohmann | Colorado Rockies | Kansas City Royals | Trade |
| Jul 31, 2006 | Trade | Jeremy Affeldt | Kansas City Royals | Colorado Rockies | Trade |
| Jul 31, 2006 | Trade | Denny Bautista | Kansas City Royals | Colorado Rockies | Trade |
| Jul 30, 2006 | Trade | Bryan Corey | Texas Rangers | Boston Red Sox | Trade |
| Jul 30, 2006 | Trade | Luis Mendoza | Boston Red Sox | Texas Rangers | Trade |
| Jul 30, 2006 | Trade | Ronnie Belliard | Cleveland Indians | St. Louis Cardinals | Trade |
| Jul 30, 2006 | Trade | Hector Luna | St. Louis Cardinals | Cleveland Indians | Trade |
| Jul 30, 2006 | Trade | Bobby Abreu | Philadelphia Phillies | New York Yankees | Trade |
| Jul 30, 2006 | Trade | Cory Lidle | Philadelphia Phillies | New York Yankees | Trade |
| Jul 30, 2006 | Trade | C.J. Henry | New York Yankees | Philadelphia Phillies | Trade |
| Jul 30, 2006 | Trade | Matt Smith | New York Yankees | Philadelphia Phillies | Trade |
| Jul 30, 2006 | Trade | Jesus Sanchez | New York Yankees | Philadelphia Phillies | Trade |
| Jul 30, 2006 | Trade | Carlos Monasterios | New York Yankees | Philadelphia Phillies | Trade |
| Jul 28, 2006 | Signed as free agent | Brandon Puffer | — | Oakland Athletics | Free agent signing |
| Jul 28, 2006 | Released | Tike Redman | Detroit Tigers | — | Release |
| Jul 28, 2006 | Trade | Mike Stanton | Washington Nationals | San Francisco Giants | Trade |
| Jul 28, 2006 | Trade | Shairon Martis | San Francisco Giants | Washington Nationals | Trade |
| Jul 28, 2006 | Trade | Carlos Lee | Milwaukee Brewers | Texas Rangers | Trade |
| Jul 28, 2006 | Trade | Nelson Cruz | Milwaukee Brewers | Texas Rangers | Trade |
| Jul 28, 2006 | Trade | Laynce Nix | Texas Rangers | Milwaukee Brewers | Trade |
| Jul 28, 2006 | Trade | Kevin Mench | Texas Rangers | Milwaukee Brewers | Trade |
| Jul 28, 2006 | Trade | Francisco Cordero | Texas Rangers | Milwaukee Brewers | Trade |
| Jul 28, 2006 | Trade | Julian Cordero | Texas Rangers | Milwaukee Brewers | Trade |
| Jul 28, 2006 | Trade | David Bell | Philadelphia Phillies | Milwaukee Brewers | Trade |
| Jul 28, 2006 | Trade | Wilfrido Laureano | Milwaukee Brewers | Philadelphia Phillies | Trade |
| Jul 28, 2006 | Trade | Unnamed | Los Angeles Dodgers | Atlanta Braves | $ |
| Jul 28, 2006 | Trade | Danys Baez | Los Angeles Dodgers | Atlanta Braves | Trade |
| Jul 28, 2006 | Trade | Willy Aybar | Los Angeles Dodgers | Atlanta Braves | Trade |
| Jul 28, 2006 | Trade | Wilson Betemit | Atlanta Braves | Los Angeles Dodgers | Trade |
| Jul 27, 2006 | Signed as free agent | Esteban Yan | — | Kansas City Royals | Free agent signing |
| Jul 26, 2006 | Released | Matt Anderson | San Francisco Giants | — | Release |
| Jul 26, 2006 | Released | Carl Everett | Seattle Mariners | — | Release |
| Jul 26, 2006 | Released | Kelly Stinnett | New York Yankees | — | Release |
| Jul 26, 2006 | Trade | Unnamed | Cleveland Indians | Seattle Mariners | $ |
| Jul 26, 2006 | Trade | Ben Broussard | Cleveland Indians | Seattle Mariners | Trade |
| Jul 26, 2006 | Trade | Shin-Soo Choo | Seattle Mariners | Cleveland Indians | Trade |
| Jul 26, 2006 | Trade | Hector Made | New York Yankees | Philadelphia Phillies | Trade |
| Jul 26, 2006 | Trade | Sal Fasano | Philadelphia Phillies | New York Yankees | Trade |
| Jul 25, 2006 | Released | Brandon Puffer | Houston Astros | — | Release |
| Jul 25, 2006 | Signed as free agent | Ricardo Rodriguez | — | St. Louis Cardinals | Free agent signing |
| Jul 25, 2006 | Trade | Unnamed | Los Angeles Dodgers | Kansas City Royals | $ |
| Jul 25, 2006 | Trade | Odalis Perez | Los Angeles Dodgers | Kansas City Royals | Trade |
| Jul 25, 2006 | Trade | Blake Johnson | Los Angeles Dodgers | Kansas City Royals | Trade |
| Jul 25, 2006 | Trade | Julio Pimentel | Los Angeles Dodgers | Kansas City Royals | Trade |
| Jul 25, 2006 | Trade | Elmer Dessens | Kansas City Royals | Los Angeles Dodgers | Trade |
| Jul 25, 2006 | Trade | Tony Graffanino | Kansas City Royals | Milwaukee Brewers | Trade |
| Jul 25, 2006 | Trade | Jorge De La Rosa | Milwaukee Brewers | Kansas City Royals | Trade |
| Jul 24, 2006 | Signed as free agent | Ben Howard | — | Toronto Blue Jays | Free agent signing |
| Jul 24, 2006 | Released | Eric Junge | San Diego Padres | — | Release |
| Jul 24, 2006 | Released | Phil Norton | Chicago Cubs | — | Release |
| Jul 24, 2006 | Released | Chris Widger | Chicago White Sox | — | Release |
| Jul 24, 2006 | Trade | Mike MacDougal | Kansas City Royals | Chicago White Sox | Trade |
| Jul 24, 2006 | Trade | Tyler Lumsden | Chicago White Sox | Kansas City Royals | Trade |
| Jul 24, 2006 | Trade | Dan Cortes | Chicago White Sox | Kansas City Royals | Trade |
| Jul 23, 2006 | Trade | Sandy Alomar | Los Angeles Dodgers | Chicago White Sox | Trade |
| Jul 23, 2006 | Trade | B.J. LaMura | Chicago White Sox | Los Angeles Dodgers | Trade |
| Jul 22, 2006 | Released | Jesus Feliciano | Washington Nationals | — | Release |
| Jul 22, 2006 | Released | Ricardo Rodriguez | Atlanta Braves | — | Release |
| Jul 22, 2006 | Signed as free agent | Andy Van Hekken | — | Kansas City Royals | Free agent signing |
| Jul 22, 2006 | Trade | Shea Hillenbrand | Toronto Blue Jays | San Francisco Giants | Trade |
| Jul 22, 2006 | Trade | Vinnie Chulk | Toronto Blue Jays | San Francisco Giants | Trade |
| Jul 22, 2006 | Trade | Jeremy Accardo | San Francisco Giants | Toronto Blue Jays | Trade |
| Jul 22, 2006 | Trade | Scott Williamson | Chicago Cubs | San Diego Padres | Trade |
| Jul 22, 2006 | Trade | Fabian Jimenez Angulo | San Diego Padres | Chicago Cubs | Trade |
| Jul 22, 2006 | Trade | Joel Santo | San Diego Padres | Chicago Cubs | Trade |
| Jul 21, 2006 | Signed as free agent | Quinton McCracken | — | Minnesota Twins | Free agent signing |
| Jul 21, 2006 | Trade | Randy Newsom | Boston Red Sox | Cleveland Indians | Trade |
| Jul 20, 2006 | Signed as free agent | Chad Bentz | — | Cincinnati Reds | Free agent signing |
| Jul 20, 2006 | Released | Cliff Politte | Chicago White Sox | — | Release |
| Jul 20, 2006 | Signed as free agent | Mike Venafro | — | Colorado Rockies | Free agent signing |
| Jul 20, 2006 | Trade | Bob Wickman | Cleveland Indians | Atlanta Braves | Trade |
| Jul 20, 2006 | Trade | Max Ramirez | Atlanta Braves | Cleveland Indians | Trade |
| Jul 19, 2006 | Released | Vinny Castilla | San Diego Padres | — | Release |
| Jul 19, 2006 | Released | Aquilino Lopez | San Diego Padres | — | Release |
| Jul 19, 2006 | Trade | Justin Ruggiano | Los Angeles Dodgers | Tampa Bay Devil Rays | Trade |
| Jul 19, 2006 | Trade | Jeff Keppinger | New York Mets | Kansas City Royals | Trade |
| Jul 19, 2006 | Trade | Ruben Gotay | Kansas City Royals | New York Mets | Trade |
| Jul 18, 2006 | Signed | Randall Delgado | — | Atlanta Braves | Amateur free agent signing |
| Jul 18, 2006 | Trade | Brian Sikorski | San Diego Padres | Cleveland Indians | Trade |
| Jul 18, 2006 | Trade | Mike Adams | Cleveland Indians | San Diego Padres | Trade |
| Jul 17, 2006 | Signed as free agent | Brian Boehringer | — | Detroit Tigers | Free agent signing |
| Jul 17, 2006 | Released | John Gall | St. Louis Cardinals | — | Release |
| Jul 16, 2006 | Released | Ben Howard | Cleveland Indians | — | Release |
| Jul 15, 2006 | Signed as free agent | Julius Matos | — | San Diego Padres | Free agent signing |
| Jul 15, 2006 | Released | Scott Seabol | Florida Marlins | — | Release |
| Jul 15, 2006 | Released | Mike Venafro | Cincinnati Reds | — | Release |
| Jul 14, 2006 | Signed as free agent | Adam Bernero | — | Kansas City Royals | Free agent signing |
| Jul 14, 2006 | Signed as free agent | Erubiel Durazo | — | Minnesota Twins | Free agent signing |
| Jul 14, 2006 | Signed as free agent | Luis Matos | — | Washington Nationals | Free agent signing |
| Jul 14, 2006 | Signed as free agent | Adam Pettyjohn | — | Oakland Athletics | Free agent signing |
| Jul 14, 2006 | Signed as free agent | Sidney Ponson | — | New York Yankees | Free agent signing |
| Jul 14, 2006 | Released | Esteban Yan | Cincinnati Reds | — | Release |
| Jul 13, 2006 | Released | Adam Bernero | Philadelphia Phillies | — | Release |
| Jul 13, 2006 | Released | Brian Boehringer | Kansas City Royals | — | Release |
| Jul 13, 2006 | Released | Jason Romano | Tampa Bay Devil Rays | — | Release |
| Jul 13, 2006 | Trade | Austin Kearns | Cincinnati Reds | Washington Nationals | Trade |
| Jul 13, 2006 | Trade | Felipe Lopez | Cincinnati Reds | Washington Nationals | Trade |
| Jul 13, 2006 | Trade | Ryan Wagner | Cincinnati Reds | Washington Nationals | Trade |
| Jul 13, 2006 | Trade | Gary Majewski | Washington Nationals | Cincinnati Reds | Trade |
| Jul 13, 2006 | Trade | Royce Clayton | Washington Nationals | Cincinnati Reds | Trade |
| Jul 13, 2006 | Trade | Bill Bray | Washington Nationals | Cincinnati Reds | Trade |
| Jul 13, 2006 | Trade | Brendan Harris | Washington Nationals | Cincinnati Reds | Trade |
| Jul 13, 2006 | Trade | Daryl Thompson | Washington Nationals | Cincinnati Reds | Trade |
| Jul 12, 2006 | Signed as free agent | Dusty Bergman | — | San Francisco Giants | Free agent signing |
| Jul 12, 2006 | Signed | Hector Sanchez | — | San Francisco Giants | Amateur free agent signing |
| Jul 12, 2006 | Trade | Unnamed | Tampa Bay Devil Rays | Houston Astros | $ |
| Jul 12, 2006 | Trade | Aubrey Huff | Tampa Bay Devil Rays | Houston Astros | Trade |
| Jul 12, 2006 | Trade | Ben Zobrist | Houston Astros | Tampa Bay Devil Rays | Trade |
| Jul 12, 2006 | Trade | Mitch Talbot | Houston Astros | Tampa Bay Devil Rays | Trade |
| Jul 11, 2006 | Signed | Wilmer Font | — | Texas Rangers | Amateur free agent signing |
| Jul 11, 2006 | Signed | Ruben Tejada | — | New York Mets | Amateur free agent signing |
| Jul 10, 2006 | Released | Dusty Bergman | New York Yankees | — | Release |
| Jul 10, 2006 | Released | Ruben Sierra | Minnesota Twins | — | Release |
| Jul 10, 2006 | Signed | Wilfredo Boscan | — | Texas Rangers | Amateur free agent signing |
| Jul 9, 2006 | Released | Matt Duff | Toronto Blue Jays | — | Release |
| Jul 9, 2006 | Released | Dave Elder | Kansas City Royals | — | Release |
| Jul 9, 2006 | Signed as free agent | Matt Ginter | — | Pittsburgh Pirates | Free agent signing |
| Jul 8, 2006 | Signed | Francisco Peña | — | New York Mets | Amateur free agent signing |
| Jul 7, 2006 | Signed as free agent | Jason Karnuth | — | Detroit Tigers | Free agent signing |
| Jul 7, 2006 | Released | Hector Mercado | Detroit Tigers | — | Release |
| Jul 7, 2006 | Released | Sidney Ponson | St. Louis Cardinals | — | Release |
| Jul 7, 2006 | Signed as free agent | Pedro Swann | — | Philadelphia Phillies | Free agent signing |
| Jul 6, 2006 | Released | Luis Matos | Baltimore Orioles | — | Release |
| Jul 6, 2006 | Released | Quinton McCracken | Cincinnati Reds | — | Release |
| Jul 6, 2006 | Trade | Unnamed | Seattle Mariners | Cincinnati Reds | $ |
| Jul 6, 2006 | Trade | Eddie Guardado | Seattle Mariners | Cincinnati Reds | Trade |
| Jul 6, 2006 | Trade | Travis Chick | Cincinnati Reds | Seattle Mariners | Trade |
| Jul 5, 2006 | Signed as free agent | David Lee | — | Florida Marlins | Free agent signing |
| Jul 5, 2006 | Trade | Unnamed | Los Angeles Angels of Anaheim | St. Louis Cardinals | $ |
| Jul 5, 2006 | Trade | Jeff Weaver | Los Angeles Angels of Anaheim | St. Louis Cardinals | Trade |
| Jul 5, 2006 | Trade | Terry Evans | St. Louis Cardinals | Los Angeles Angels of Anaheim | Trade |
| Jul 4, 2006 | Released | David Lee | Houston Astros | — | Release |
| Jul 3, 2006 | Signed | Jose Ortega | — | Detroit Tigers | Amateur free agent signing |
| Jul 3, 2006 | Signed as free agent | John Stephens | — | Philadelphia Phillies | Free agent signing |
| Jul 3, 2006 | Signed as free agent | Joe Valentine | — | Milwaukee Brewers | Free agent signing |
| Jul 3, 2006 | Signed | Danny Salazar | — | Cleveland Indians | Amateur free agent signing |
| Jul 3, 2006 | Signed | Jorge Rondon | — | St. Louis Cardinals | Amateur free agent signing |
| Jul 2, 2006 | Released | Erubiel Durazo | New York Yankees | — | Release |
| Jul 2, 2006 | Signed | Freddy Galvis | — | Philadelphia Phillies | Amateur free agent signing |
| Jul 2, 2006 | Signed | Jimmy Paredes | — | New York Yankees | Amateur free agent signing |
| Jul 2, 2006 | Released | Julio Ramirez | New York Mets | — | Release |
| Jul 2, 2006 | Signed | Cesar Hernandez | — | Philadelphia Phillies | Amateur free agent signing |
| Jul 2, 2006 | Signed | Engel Beltre | — | Boston Red Sox | Amateur free agent signing |
| Jul 2, 2006 | Signed | Stolmy Pimentel | — | Boston Red Sox | Amateur free agent signing |
| Jul 2, 2006 | Signed | Jose Pirela | — | New York Yankees | Amateur free agent signing |
| Jul 2, 2006 | Signed | Albert Suarez | — | Tampa Bay Devil Rays | Amateur free agent signing |
| Jul 2, 2006 | Signed | Francisco Arcia | — | New York Yankees | Amateur free agent signing |
| Jul 1, 2006 | Signed as free agent | Brian Bruney | — | New York Yankees | Free agent signing |
| Jul 1, 2006 | Released | Matt Ginter | Boston Red Sox | — | Release |
| Jul 1, 2006 | Released | Jason Karnuth | Oakland Athletics | — | Release |
| Jul 1, 2006 | Released | Santiago Ramirez | Washington Nationals | — | Release |
| Jul 1, 2006 | Trade | Tim Olson | Texas Rangers | Toronto Blue Jays | Trade |
| Jul 1, 2006 | Trade | Joey McLaughlin | Toronto Blue Jays | Texas Rangers | Trade |
| Jun 30, 2006 | Released | Tony Womack | Chicago Cubs | — | Release |
| Jun 30, 2006 | Trade | Eduardo Perez | Cleveland Indians | Seattle Mariners | Trade |
| Jun 30, 2006 | Trade | Asdrubal Cabrera | Seattle Mariners | Cleveland Indians | Trade |
| Jun 29, 2006 | Released | Chad Bentz | Chicago White Sox | — | Release |
| Jun 29, 2006 | Released | Marshall McDougall | Texas Rangers | — | Release |
| Jun 29, 2006 | Released | Ben Weber | Toronto Blue Jays | — | Release |
| Jun 29, 2006 | Trade | Unnamed | Philadelphia Phillies | Texas Rangers | $ |
| Jun 29, 2006 | Trade | Daniel Haigwood | Philadelphia Phillies | Texas Rangers | Trade |
| Jun 29, 2006 | Trade | Fabio Castro | Texas Rangers | Philadelphia Phillies | Trade |
| Jun 28, 2006 | Signed as free agent | Dustan Mohr | — | Detroit Tigers | Free agent signing |
| Jun 28, 2006 | Released | John Stephens | Baltimore Orioles | — | Release |
| Jun 27, 2006 | Trade | Unnamed | Tampa Bay Devil Rays | Los Angeles Dodgers | $ |
| Jun 27, 2006 | Trade | Toby Hall | Tampa Bay Devil Rays | Los Angeles Dodgers | Trade |
| Jun 27, 2006 | Trade | Mark Hendrickson | Tampa Bay Devil Rays | Los Angeles Dodgers | Trade |
| Jun 27, 2006 | Trade | Dioner Navarro | Los Angeles Dodgers | Tampa Bay Devil Rays | Trade |
| Jun 27, 2006 | Trade | Jae Weong Seo | Los Angeles Dodgers | Tampa Bay Devil Rays | Trade |
| Jun 26, 2006 | Released | Will Cunnane | St. Louis Cardinals | — | Release |
| Jun 25, 2006 | Signed as free agent | Russ Ortiz | — | Baltimore Orioles | Free agent signing |
| Jun 25, 2006 | Released | Mike Remlinger | Atlanta Braves | — | Release |
| Jun 24, 2006 | Released | Dave Coggin | Atlanta Braves | — | Release |
| Jun 23, 2006 | Signed as free agent | Mike Cervenak | — | San Francisco Giants | Free agent signing |
| Jun 23, 2006 | Signed as free agent | Bo Hart | — | St. Louis Cardinals | Free agent signing |
| Jun 23, 2006 | Signed as free agent | D'Angelo Jimenez | — | Oakland Athletics | Free agent signing |
| Jun 23, 2006 | Released | Tim Laker | Cleveland Indians | — | Release |
| Jun 23, 2006 | Signed as free agent | Kevin Olsen | — | Oakland Athletics | Free agent signing |
| Jun 23, 2006 | Released | John Riedling | St. Louis Cardinals | — | Release |
| Jun 22, 2006 | Signed as free agent | Nathan Haynes | — | Los Angeles Angels of Anaheim | Free agent signing |
| Jun 21, 2006 | Released | Terry Mulholland | Arizona Diamondbacks | — | Release |
| Jun 21, 2006 | Released | Adam Pettyjohn | Seattle Mariners | — | Release |
| Jun 21, 2006 | Signed as free agent | Jason Romano | — | Tampa Bay Devil Rays | Free agent signing |
| Jun 21, 2006 | Signed as free agent | Todd Sears | — | Florida Marlins | Free agent signing |
| Jun 21, 2006 | Released | Joe Valentine | Houston Astros | — | Release |
| Jun 21, 2006 | Released | Dan Wright | Seattle Mariners | — | Release |
| Jun 20, 2006 | Signed as free agent | Jared Sandberg | — | Cleveland Indians | Free agent signing |
| Jun 20, 2006 | Trade | Joey Gathright | Tampa Bay Devil Rays | Kansas City Royals | Trade |
| Jun 20, 2006 | Trade | Fernando Cortez | Tampa Bay Devil Rays | Kansas City Royals | Trade |
| Jun 20, 2006 | Trade | J. P. Howell | Kansas City Royals | Tampa Bay Devil Rays | Trade |
| Jun 19, 2006 | Released | David Kelton | Atlanta Braves | — | Release |
| Jun 19, 2006 | Signed as free agent | Scott Sauerbeck | — | Oakland Athletics | Free agent signing |
| Jun 19, 2006 | Released | J. T. Snow | Boston Red Sox | — | Release |
| Jun 17, 2006 | Signed as free agent | Frank Brooks | — | Boston Red Sox | Free agent signing |
| Jun 17, 2006 | Released | Bo Hart | Colorado Rockies | — | Release |
| Jun 17, 2006 | Signed as free agent | Andrew Lorraine | — | Chicago White Sox | Free agent signing |
| Jun 16, 2006 | Released | Rhiner Cruz | Detroit Tigers | — | Release |
| Jun 16, 2006 | Signed | Rob Delaney | — | Minnesota Twins | Amateur free agent signing |
| Jun 16, 2006 | Released | John Halama | Baltimore Orioles | — | Release |
| Jun 16, 2006 | Released | Mike Holtz | Boston Red Sox | — | Release |
| Jun 15, 2006 | Signed as free agent | Steve Andrade | — | San Diego Padres | Free agent signing |
| Jun 15, 2006 | Released | Danny Klassen | Houston Astros | — | Release |
| Jun 15, 2006 | Released | Alex Sanchez | Cincinnati Reds | — | Release |
| Jun 15, 2006 | Released | Jimmy Serrano | Boston Red Sox | — | Release |
| Jun 15, 2006 | Trade | Juan Castro | Minnesota Twins | Cincinnati Reds | Trade |
| Jun 15, 2006 | Trade | Brandon Roberts | Cincinnati Reds | Minnesota Twins | Trade |
| Jun 15, 2006 | Trade | David Riske | Boston Red Sox | Chicago White Sox | Trade |
| Jun 15, 2006 | Trade | Javier Lopez | Chicago White Sox | Boston Red Sox | Trade |
| Jun 14, 2006 | Released | Tony Batista | Minnesota Twins | — | Release |
| Jun 14, 2006 | Signed as free agent | Jason Conti | — | St. Louis Cardinals | Free agent signing |
| Jun 14, 2006 | Released | D'Angelo Jimenez | Texas Rangers | — | Release |
| Jun 14, 2006 | Released | Scott Sauerbeck | Cleveland Indians | — | Release |
| Jun 13, 2006 | Released | Jason Conti | New York Yankees | — | Release |
| Jun 13, 2006 | Signed as free agent | Valerio De Los Santos | — | Chicago White Sox | Free agent signing |
| Jun 13, 2006 | Signed as free agent | Bart Miadich | — | Florida Marlins | Free agent signing |
| Jun 13, 2006 | Released | Russ Ortiz | Arizona Diamondbacks | — | Release |
| Jun 13, 2006 | Released | Rob Sasser | Chicago White Sox | — | Release |
| Jun 13, 2006 | Trade | Jeff Stevens | Cincinnati Reds | Cleveland Indians | Trade |
| Jun 12, 2006 | Released | Edgardo Alfonzo | Toronto Blue Jays | — | Release |
| Jun 12, 2006 | Released | Frank Brooks | Kansas City Royals | — | Release |
| Jun 12, 2006 | Released | Tony Fiore | Detroit Tigers | — | Release |
| Jun 12, 2006 | Released | Todd Sears | Seattle Mariners | — | Release |
| Jun 11, 2006 | Released | Scott Erickson | New York Yankees | — | Release |
| Jun 10, 2006 | Released | Todd Self | New York Yankees | — | Release |
| Jun 10, 2006 | Signed as free agent | Jose De La Torre | — | New York Mets | Free agent signing |
| Jun 9, 2006 | Released | Antonio Alfonseca | Texas Rangers | — | Release |
| Jun 9, 2006 | Released | Steve Andrade | Kansas City Royals | — | Release |
| Jun 9, 2006 | Signed as free agent | Adam Greenberg | — | Los Angeles Dodgers | Free agent signing |
| Jun 9, 2006 | Released | Bart Miadich | Tampa Bay Devil Rays | — | Release |
| Jun 9, 2006 | Signed as free agent | Donovan Osborne | — | Kansas City Royals | Free agent signing |
| Jun 9, 2006 | Trade | Unnamed | New York Mets | Colorado Rockies | $ |
| Jun 9, 2006 | Trade | Kazuo Matsui | New York Mets | Colorado Rockies | Trade |
| Jun 9, 2006 | Trade | Eli Marrero | Colorado Rockies | New York Mets | Trade |
| Jun 8, 2006 | Signed as free agent | Adam Bernero | — | Philadelphia Phillies | Free agent signing |
| Jun 8, 2006 | Signed as free agent | Matt Skrmetta | — | Chicago White Sox | Free agent signing |
| Jun 7, 2006 | Signed as free agent | Jason Alfaro | — | Cleveland Indians | Free agent signing |
| Jun 7, 2006 | Released | Alejandro Freire | Baltimore Orioles | — | Release |
| Jun 7, 2006 | Released | Jason Grimsley | Arizona Diamondbacks | — | Release |
| Jun 7, 2006 | Released | Hideo Nomo | Chicago White Sox | — | Release |
| Jun 7, 2006 | Released | Damian Rolls | Chicago White Sox | — | Release |
| Jun 7, 2006 | Signed as free agent | Bob Smith | — | Chicago White Sox | Free agent signing |
| Jun 6, 2006 | Released | Jason Alfaro | Pittsburgh Pirates | — | Release |
| Jun 6, 2006 | Released | Adam Johnson | Oakland Athletics | — | Release |
| Jun 5, 2006 | Signed as free agent | Chris Truby | — | Pittsburgh Pirates | Free agent signing |
| Jun 4, 2006 | Signed as free agent | Walter Young | — | Houston Astros | Free agent signing |
| Jun 2, 2006 | Released | Kevin Appier | Seattle Mariners | — | Release |
| Jun 2, 2006 | Released | Adam Bernero | Kansas City Royals | — | Release |
| Jun 2, 2006 | Released | Adam Greenberg | Chicago Cubs | — | Release |
| Jun 1, 2006 | Released | Darrell May | Cincinnati Reds | — | Release |
| Jun 1, 2006 | Trade | Ben Kozlowski | Cincinnati Reds | Los Angeles Dodgers | Trade |
| May 31, 2006 | Signed as free agent | Roger Clemens | — | Houston Astros | Free agent signing |
| May 31, 2006 | Signed as free agent | Prentice Redman | — | Washington Nationals | Free agent signing |
| May 31, 2006 | Released | Chris Truby | Los Angeles Dodgers | — | Release |
| May 31, 2006 | Trade | Unnamed | Texas Rangers | Chicago Cubs | $ |
| May 31, 2006 | Trade | Phil Nevin | Texas Rangers | Chicago Cubs | Trade |
| May 31, 2006 | Trade | Jerry Hairston | Chicago Cubs | Texas Rangers | Trade |
| May 30, 2006 | Signed as free agent | Jacob Cruz | — | New York Mets | Free agent signing |
| May 30, 2006 | Signed as free agent | Mike Difelice | — | New York Mets | Free agent signing |
| May 30, 2006 | Released | Matt Lawton | Seattle Mariners | — | Release |
| May 30, 2006 | Trade | Unnamed | Los Angeles Angels of Anaheim | Cincinnati Reds | $ |
| May 30, 2006 | Trade | Esteban Yan | Los Angeles Angels of Anaheim | Cincinnati Reds | Trade |
| May 30, 2006 | Trade | Kyle Edens | Cincinnati Reds | Los Angeles Angels of Anaheim | Trade |
| May 30, 2006 | Signed | Jorge De Leon | — | Houston Astros | Amateur free agent signing |
| May 29, 2006 | Signed | Darren O'Day | — | Los Angeles Angels of Anaheim | Amateur free agent signing |
| May 29, 2006 | Released | Andy Pratt | Milwaukee Brewers | — | Release |
| May 28, 2006 | Signed as free agent | Ryan Jensen | — | Texas Rangers | Free agent signing |
| May 28, 2006 | Released | Desi Relaford | St. Louis Cardinals | — | Release |
| May 27, 2006 | Signed as free agent | Brian Boehringer | — | Kansas City Royals | Free agent signing |
| May 27, 2006 | Signed as free agent | Travis Smith | — | St. Louis Cardinals | Free agent signing |
| May 26, 2006 | Signed as free agent | Tim Raines | — | Washington Nationals | Free agent signing |
| May 26, 2006 | Trade | Geremi Gonzalez | New York Mets | Milwaukee Brewers | Trade |
| May 26, 2006 | Trade | Mike Adams | Milwaukee Brewers | New York Mets | Trade |
| May 26, 2006 | Signed | Zach Clark | — | Baltimore Orioles | Amateur free agent signing |
| May 25, 2006 | Signed as free agent | Edgardo Alfonzo | — | Toronto Blue Jays | Free agent signing |
| May 25, 2006 | Released | Matt Mantei | Detroit Tigers | — | Release |
| May 25, 2006 | Signed as free agent | Orber Moreno | — | St. Louis Cardinals | Free agent signing |
| May 25, 2006 | Released | Mike Rose | Tampa Bay Devil Rays | — | Release |
| May 25, 2006 | Signed as free agent | Mike Rose | — | St. Louis Cardinals | Free agent signing |
| May 25, 2006 | Released | Jared Sandberg | Houston Astros | — | Release |
| May 25, 2006 | Released | Brad Voyles | St. Louis Cardinals | — | Release |
| May 25, 2006 | Trade | Unnamed | Cincinnati Reds | New York Mets | $ |
| May 25, 2006 | Trade | David Williams | Cincinnati Reds | New York Mets | Trade |
| May 25, 2006 | Trade | Robert Manuel | New York Mets | Cincinnati Reds | Trade |
| May 24, 2006 | Signed as free agent | Jonathan Johnson | — | Atlanta Braves | Free agent signing |
| May 24, 2006 | Signed as free agent | Neal Musser | — | Kansas City Royals | Free agent signing |
| May 24, 2006 | Trade | Orlando Hernandez | Arizona Diamondbacks | New York Mets | Trade |
| May 24, 2006 | Trade | Jorge Julio | New York Mets | Arizona Diamondbacks | Trade |
| May 23, 2006 | Released | Aaron Holbert | Cincinnati Reds | — | Release |
| May 23, 2006 | Released | Neal Musser | Arizona Diamondbacks | — | Release |
| May 22, 2006 | Released | Eric Crozier | Cincinnati Reds | — | Release |
| May 22, 2006 | Signed | Blake Lalli | — | Chicago Cubs | Amateur free agent signing |
| May 22, 2006 | Signed as free agent | Blaine Neal | — | Pittsburgh Pirates | Free agent signing |
| May 21, 2006 | Released | Edgardo Alfonzo | Los Angeles Angels of Anaheim | — | Release |
| May 21, 2006 | Signed as free agent | Erubiel Durazo | — | New York Yankees | Free agent signing |
| May 21, 2006 | Released | Esix Snead | Baltimore Orioles | — | Release |
| May 20, 2006 | Released | Brian Bruney | Arizona Diamondbacks | — | Release |
| May 19, 2006 | Released | Brian Buchanan | Cincinnati Reds | — | Release |
| May 19, 2006 | Released | Bartolome Fortunato | New York Mets | — | Release |
| May 19, 2006 | Signed as free agent | Joe Mays | — | Cincinnati Reds | Free agent signing |
| May 18, 2006 | Signed as free agent | Cory Aldridge | — | Chicago White Sox | Free agent signing |
| May 18, 2006 | Released | Buddy Carlyle | Florida Marlins | — | Release |
| May 18, 2006 | Signed as free agent | Terrence Long | — | New York Yankees | Free agent signing |
| May 18, 2006 | Released | Prentice Redman | St. Louis Cardinals | — | Release |
| May 18, 2006 | Signed as free agent | Tony Torcato | — | Chicago White Sox | Free agent signing |
| May 18, 2006 | Signed as free agent | Tony Womack | — | Chicago Cubs | Free agent signing |
| May 17, 2006 | Released | Erubiel Durazo | Texas Rangers | — | Release |
| May 17, 2006 | Released | Raul Valdes | Chicago Cubs | — | Release |
| May 15, 2006 | Released | Cory Aldridge | New York Mets | — | Release |
| May 15, 2006 | Signed as free agent | Stephen Smitherman | — | San Diego Padres | Free agent signing |
| May 14, 2006 | Released | Eric Valent | San Diego Padres | — | Release |
| May 14, 2006 | Trade | Brad Baker | Atlanta Braves | Boston Red Sox | Trade |
| May 13, 2006 | Signed as free agent | Dave Berg | — | Texas Rangers | Free agent signing |
| May 13, 2006 | Released | Ryan Snare | Kansas City Royals | — | Release |
| May 13, 2006 | Trade | Unnamed | Milwaukee Brewers | Texas Rangers | $ |
| May 13, 2006 | Trade | Enrique Cruz | Milwaukee Brewers | Texas Rangers | Trade |
| May 13, 2006 | Trade | Brian Shouse | Texas Rangers | Milwaukee Brewers | Trade |
| May 12, 2006 | Released | Jung Bong | Cincinnati Reds | — | Release |
| May 12, 2006 | Released | Felix Heredia | Cleveland Indians | — | Release |
| May 12, 2006 | Signed as free agent | Travis Phelps | — | Milwaukee Brewers | Free agent signing |
| May 12, 2006 | Signed as free agent | Todd Self | — | New York Yankees | Free agent signing |
| May 11, 2006 | Signed as free agent | Jim Brower | — | San Diego Padres | Free agent signing |
| May 11, 2006 | Signed as free agent | Matt Perisho | — | St. Louis Cardinals | Free agent signing |
| May 11, 2006 | Trade | Freddy Guzman | San Diego Padres | Texas Rangers | Trade |
| May 11, 2006 | Trade | Cesar Rojas | San Diego Padres | Texas Rangers | Trade |
| May 11, 2006 | Trade | John Hudgins | Texas Rangers | San Diego Padres | Trade |
| May 11, 2006 | Trade | Vince Sinisi | Texas Rangers | San Diego Padres | Trade |
| May 10, 2006 | Signed as free agent | Jeriome Robertson | — | New York Mets | Free agent signing |
| May 10, 2006 | Signed as free agent | Damian Rolls | — | Chicago White Sox | Free agent signing |
| May 9, 2006 | Signed as free agent | Giovanni Carrara | — | Los Angeles Dodgers | Free agent signing |
| May 9, 2006 | Signed as free agent | Nelson Figueroa | — | Washington Nationals | Free agent signing |
| May 9, 2006 | Released | Jose Silva | Texas Rangers | — | Release |
| May 8, 2006 | Signed as free agent | Matt Blank | — | Florida Marlins | Free agent signing |
| May 8, 2006 | Released | Jeff Fassero | San Francisco Giants | — | Release |
| May 8, 2006 | Released | Joe Mays | Kansas City Royals | — | Release |
| May 8, 2006 | Signed | Simon Castro | — | San Diego Padres | Amateur free agent signing |
| May 5, 2006 | Signed | Greg Infante | — | Chicago White Sox | Amateur free agent signing |
| May 5, 2006 | Released | Terrence Long | Cincinnati Reds | — | Release |
| May 5, 2006 | Signed | Juan Lagares | — | New York Mets | Amateur free agent signing |
| May 3, 2006 | Released | Chris Saenz | Milwaukee Brewers | — | Release |
| May 3, 2006 | Released | Todd Self | New York Mets | — | Release |
| May 3, 2006 | Signed as free agent | Tyler Yates | — | Atlanta Braves | Free agent signing |
| May 2, 2006 | Released | Jim Brower | Baltimore Orioles | — | Release |
| May 2, 2006 | Signed as free agent | Vic Darensbourg | — | Cleveland Indians | Free agent signing |
| May 2, 2006 | Released | Tom Gregorio | Seattle Mariners | — | Release |
| May 2, 2006 | Signed as free agent | Tom Gregorio | — | Texas Rangers | Free agent signing |
| May 2, 2006 | Signed as free agent | Jeff Nelson | — | Chicago White Sox | Free agent signing |
| May 1, 2006 | Released | Damian Rolls | New York Yankees | — | Release |
| May 1, 2006 | Trade | Unnamed | Boston Red Sox | San Diego Padres | $ |
| May 1, 2006 | Trade | Cla Meredith | Boston Red Sox | San Diego Padres | Trade |
| May 1, 2006 | Trade | Josh Bard | Boston Red Sox | San Diego Padres | Trade |
| May 1, 2006 | Trade | Doug Mirabelli | San Diego Padres | Boston Red Sox | Trade |
| Apr 29, 2006 | Signed as free agent | Alex Prieto | — | Kansas City Royals | Free agent signing |
| Apr 28, 2006 | Released | Kevin Orie | Houston Astros | — | Release |
| Apr 28, 2006 | Released | Matt Perisho | Baltimore Orioles | — | Release |
| Apr 28, 2006 | Signed as free agent | Jamal Strong | — | Atlanta Braves | Free agent signing |
| Apr 28, 2006 | Trade | Tyler Walker | San Francisco Giants | Tampa Bay Devil Rays | Trade |
| Apr 28, 2006 | Trade | Carlos Hines | Tampa Bay Devil Rays | San Francisco Giants | Trade |
| Apr 27, 2006 | Signed as free agent | Joe Horgan | — | Florida Marlins | Free agent signing |
| Apr 26, 2006 | Signed | Jose Quintana | — | New York Mets | Amateur free agent signing |
| Apr 26, 2006 | Signed as free agent | Chris Richard | — | Pittsburgh Pirates | Free agent signing |
| Apr 26, 2006 | Signed as free agent | Michael Tucker | — | New York Mets | Free agent signing |
| Apr 26, 2006 | Signed | Ehire Adrianza | — | San Francisco Giants | Amateur free agent signing |
| Apr 25, 2006 | Signed | Jhan Marinez | — | Florida Marlins | Amateur free agent signing |
| Apr 25, 2006 | Signed as free agent | Corky Miller | — | Boston Red Sox | Free agent signing |
| Apr 25, 2006 | Released | Ryan Rupe | Florida Marlins | — | Release |
| Apr 25, 2006 | Released | Jamal Strong | Chicago Cubs | — | Release |
| Apr 25, 2006 | Released | Walter Young | San Diego Padres | — | Release |
| Apr 24, 2006 | Released | Keith McDonald | New York Yankees | — | Release |
| Apr 24, 2006 | Released | Tony Womack | Cincinnati Reds | — | Release |
| Apr 24, 2006 | Trade | Cody Ross | Los Angeles Dodgers | Cincinnati Reds | Trade |
| Apr 23, 2006 | Released | Ricky Gutierrez | San Diego Padres | — | Release |
| Apr 23, 2006 | Released | Damian Moss | Atlanta Braves | — | Release |
| Apr 23, 2006 | Signed as free agent | Desi Relaford | — | St. Louis Cardinals | Free agent signing |
| Apr 23, 2006 | Signed as free agent | Randy Ruiz | — | New York Yankees | Free agent signing |
| Apr 22, 2006 | Released | James Baldwin | Toronto Blue Jays | — | Release |
| Apr 22, 2006 | Signed as free agent | Kerry Ligtenberg | — | Chicago Cubs | Free agent signing |
| Apr 21, 2006 | Signed as free agent | David Lee | — | Houston Astros | Free agent signing |
| Apr 20, 2006 | Signed | Juan Diaz | — | Seattle Mariners | Amateur free agent signing |
| Apr 20, 2006 | Released | Justin Miller | Tampa Bay Devil Rays | — | Release |
| Apr 20, 2006 | Signed as free agent | Tommy Phelps | — | New York Yankees | Free agent signing |
| Apr 19, 2006 | Signed as free agent | Justin Huisman | — | Houston Astros | Free agent signing |
| Apr 17, 2006 | Signed as free agent | Wayne Franklin | — | Atlanta Braves | Free agent signing |
| Apr 17, 2006 | Released | Corky Miller | Seattle Mariners | — | Release |
| Apr 17, 2006 | Released | Wes Obermueller | Atlanta Braves | — | Release |
| Apr 15, 2006 | Signed as free agent | Jesus Colome | — | New York Yankees | Free agent signing |
| Apr 15, 2006 | Released | Jayson Durocher | Texas Rangers | — | Release |
| Apr 15, 2006 | Signed as free agent | Carlos Peña | — | New York Yankees | Free agent signing |
| Apr 14, 2006 | Signed as free agent | Frank Brooks | — | Kansas City Royals | Free agent signing |
| Apr 14, 2006 | Released | Jacob Cruz | Cincinnati Reds | — | Release |
| Apr 14, 2006 | Signed as free agent | Travis Driskill | — | Houston Astros | Free agent signing |
| Apr 14, 2006 | Released | Justin Huisman | Kansas City Royals | — | Release |
| Apr 14, 2006 | Released | Frank Menechino | Cincinnati Reds | — | Release |
| Apr 14, 2006 | Released | Randy Ruiz | Kansas City Royals | — | Release |
| Apr 14, 2006 | Signed as free agent | Mike Venafro | — | Cincinnati Reds | Free agent signing |
| Apr 13, 2006 | Signed as free agent | Mike Bacsik | — | Arizona Diamondbacks | Free agent signing |
| Apr 13, 2006 | Signed as free agent | Jason Conti | — | Pittsburgh Pirates | Free agent signing |
| Apr 12, 2006 | Signed as free agent | Ricardo Rodriguez | — | Atlanta Braves | Free agent signing |
| Apr 11, 2006 | Signed as free agent | Nate Cornejo | — | Chicago White Sox | Free agent signing |
| Apr 10, 2006 | Signed as free agent | Steve Colyer | — | Colorado Rockies | Free agent signing |
| Apr 10, 2006 | Signed as free agent | Jesse Garcia | — | Houston Astros | Free agent signing |
| Apr 10, 2006 | Signed as free agent | Tike Redman | — | Detroit Tigers | Free agent signing |
| Apr 8, 2006 | Signed as free agent | Matt Perisho | — | Baltimore Orioles | Free agent signing |
| Apr 7, 2006 | Released | Vic Darensbourg | Baltimore Orioles | — | Release |
| Apr 7, 2006 | Signed as free agent | Erubiel Durazo | — | Texas Rangers | Free agent signing |
| Apr 7, 2006 | Trade | Brandon Phillips | Cleveland Indians | Cincinnati Reds | Trade |
| Apr 6, 2006 | Released | Jesus Colome | Tampa Bay Devil Rays | — | Release |
| Apr 6, 2006 | Signed as free agent | John Ennis | — | Detroit Tigers | Free agent signing |
| Apr 6, 2006 | Signed as free agent | Ricky Gutierrez | — | San Diego Padres | Free agent signing |
| Apr 6, 2006 | Signed as free agent | Carlos Hernandez | — | Houston Astros | Free agent signing |
| Apr 6, 2006 | Signed as free agent | Tomas Perez | — | Tampa Bay Devil Rays | Free agent signing |
| Apr 6, 2006 | Released | Nick Regilio | Texas Rangers | — | Release |
| Apr 6, 2006 | Signed as free agent | Luis Terrero | — | Baltimore Orioles | Free agent signing |
| Apr 6, 2006 | Trade | Marcos Carvajal | Seattle Mariners | Tampa Bay Devil Rays | Trade |
| Apr 6, 2006 | Trade | Jose De La Cruz | Tampa Bay Devil Rays | Seattle Mariners | Trade |
| Apr 5, 2006 | Released | Steve Torrealba | Cincinnati Reds | — | Release |
| Apr 5, 2006 | Trade | Franklin Nunez | Boston Red Sox | Atlanta Braves | Trade |
| Apr 4, 2006 | Signed as free agent | Edgar Gonzalez | — | Florida Marlins | Free agent signing |
| Apr 4, 2006 | Trade | Kazuhito Tadano | Cleveland Indians | Oakland Athletics | Trade |
| Apr 4, 2006 | Trade | Ramon Alvarado | Oakland Athletics | Cleveland Indians | Trade |
| Apr 3, 2006 | Signed as free agent | Kyle Phillips | — | Milwaukee Brewers | Free agent signing |
| Apr 2, 2006 | Released | Travis Driskill | Tampa Bay Devil Rays | — | Release |
| Apr 2, 2006 | Released | Wayne Franklin | Tampa Bay Devil Rays | — | Release |
| Apr 2, 2006 | Released | Matt Skrmetta | Chicago Cubs | — | Release |
| Apr 1, 2006 | Released | Brandon Kintzler | San Diego Padres | — | Release |
| Apr 1, 2006 | Signed as free agent | Darrell May | — | Cincinnati Reds | Free agent signing |
| Apr 1, 2006 | Signed as free agent | Brian Meadows | — | Tampa Bay Devil Rays | Free agent signing |
| Apr 1, 2006 | Released | Tomas Perez | Philadelphia Phillies | — | Release |
| Apr 1, 2006 | Released | Kyle Phillips | Minnesota Twins | — | Release |
| Apr 1, 2006 | Signed as free agent | John Wasdin | — | Texas Rangers | Free agent signing |
| Apr 1, 2006 | Signed as free agent | Ernie Young | — | Chicago White Sox | Free agent signing |
| Apr 1, 2006 | Trade | David Dellucci | Texas Rangers | Philadelphia Phillies | Trade |
| Apr 1, 2006 | Trade | Rob Tejeda | Philadelphia Phillies | Texas Rangers | Trade |
| Apr 1, 2006 | Trade | Jake Blalock | Philadelphia Phillies | Texas Rangers | Trade |
| Mar 31, 2006 | Released | Mike Bacsik | Washington Nationals | — | Release |
| Mar 31, 2006 | Released | Giovanni Carrara | Pittsburgh Pirates | — | Release |
| Mar 31, 2006 | Released | Edgar Gonzalez | Washington Nationals | — | Release |
| Mar 31, 2006 | Signed as free agent | Junior Herndon | — | Kansas City Royals | Free agent signing |
| Mar 31, 2006 | Released | Mark Malaska | Tampa Bay Devil Rays | — | Release |
| Mar 31, 2006 | Released | Travis Phelps | Cincinnati Reds | — | Release |
| Mar 31, 2006 | Released | Tommy Phelps | Cincinnati Reds | — | Release |
| Mar 31, 2006 | Released | Tike Redman | New York Mets | — | Release |
| Mar 31, 2006 | Released | Desi Relaford | Baltimore Orioles | — | Release |
| Mar 31, 2006 | Released | Reggie Taylor | Detroit Tigers | — | Release |
| Mar 31, 2006 | Released | Mike Venafro | New York Mets | — | Release |
| Mar 31, 2006 | Released | Keiichi Yabu | Colorado Rockies | — | Release |
| Mar 31, 2006 | Released | Tyler Yates | Baltimore Orioles | — | Release |
| Mar 31, 2006 | Trade | Unnamed | Chicago Cubs | Texas Rangers | $ |
| Mar 31, 2006 | Trade | John Rheinecker | Oakland Athletics | Texas Rangers | Trade |
| Mar 31, 2006 | Trade | Freddie Bynum | Oakland Athletics | Chicago Cubs | Trade |
| Mar 31, 2006 | Trade | Juan Dominguez | Texas Rangers | Oakland Athletics | Trade |
| Mar 31, 2006 | Trade | John Koronka | Chicago Cubs | Texas Rangers | Trade |
| Mar 31, 2006 | Trade | Wilson Valdez | Kansas City Royals | Los Angeles Dodgers | Trade |
| Mar 31, 2006 | Trade | Jarod Plummer | Los Angeles Dodgers | Kansas City Royals | Trade |
| Mar 30, 2006 | Released | Mark DiFelice | Chicago Cubs | — | Release |
| Mar 30, 2006 | Released | John Ennis | Chicago Cubs | — | Release |
| Mar 30, 2006 | Released | Jeremy Hill | New York Mets | — | Release |
| Mar 30, 2006 | Released | Matt Perisho | New York Mets | — | Release |
| Mar 30, 2006 | Released | Chris Richard | Kansas City Royals | — | Release |
| Mar 30, 2006 | Signed as free agent | Brian Sikorski | — | San Diego Padres | Free agent signing |
| Mar 30, 2006 | Released | Michael Tucker | Washington Nationals | — | Release |
| Mar 29, 2006 | Released | Deivi Cruz | St. Louis Cardinals | — | Release |
| Mar 29, 2006 | Released | Kane Davis | Milwaukee Brewers | — | Release |
| Mar 29, 2006 | Released | Geronimo Gil | Baltimore Orioles | — | Release |
| Mar 29, 2006 | Released | Lenny Harris | Florida Marlins | — | Release |
| Mar 29, 2006 | Released | Kerry Ligtenberg | Florida Marlins | — | Release |
| Mar 29, 2006 | Released | Brian Meadows | Los Angeles Dodgers | — | Release |
| Mar 29, 2006 | Released | Ricardo Rodriguez | Philadelphia Phillies | — | Release |
| Mar 29, 2006 | Signed as free agent | Jim Rushford | — | Philadelphia Phillies | Free agent signing |
| Mar 29, 2006 | Released | Luis Terrero | Arizona Diamondbacks | — | Release |
| Mar 29, 2006 | Released | John Wasdin | Texas Rangers | — | Release |
| Mar 28, 2006 | Signed as free agent | Bryan Corey | — | Texas Rangers | Free agent signing |
| Mar 28, 2006 | Released | Luther Hackman | St. Louis Cardinals | — | Release |
| Mar 28, 2006 | Signed as free agent | Felix Heredia | — | Cleveland Indians | Free agent signing |
| Mar 28, 2006 | Released | Ruben Mateo | Washington Nationals | — | Release |
| Mar 28, 2006 | Released | Jason Romano | Milwaukee Brewers | — | Release |
| Mar 28, 2006 | Trade | Aquilino Lopez | Philadelphia Phillies | San Diego Padres | Trade |
| Mar 28, 2006 | Trade | Matt Thayer | San Diego Padres | Philadelphia Phillies | Trade |
| Mar 28, 2006 | Trade | Trey Johnston | San Diego Padres | Philadelphia Phillies | Trade |
| Mar 28, 2006 | Trade | Todd Wellemeyer | Chicago Cubs | Florida Marlins | Trade |
| Mar 28, 2006 | Trade | Zach McCormack | Florida Marlins | Chicago Cubs | Trade |
| Mar 28, 2006 | Trade | Lincoln Holdzkom | Florida Marlins | Chicago Cubs | Trade |
| Mar 28, 2006 | Trade | Carlos Piste | Cincinnati Reds | Florida Marlins | Trade |
| Mar 28, 2006 | Trade | Ryan Jorgensen | Florida Marlins | Cincinnati Reds | Trade |
| Mar 27, 2006 | Released | Robert Coello | Cincinnati Reds | — | Release |
| Mar 27, 2006 | Released | Erubiel Durazo | Texas Rangers | — | Release |
| Mar 27, 2006 | Signed as free agent | Terrence Long | — | Cincinnati Reds | Free agent signing |
| Mar 27, 2006 | Released | Brian Sikorski | San Diego Padres | — | Release |
| Mar 27, 2006 | Released | Stephen Smitherman | Cincinnati Reds | — | Release |
| Mar 26, 2006 | Released | Darrell May | Minnesota Twins | — | Release |
| Mar 26, 2006 | Released | Jeff Nelson | St. Louis Cardinals | — | Release |
| Mar 26, 2006 | Released | Carlos Peña | Detroit Tigers | — | Release |
| Mar 26, 2006 | Trade | Brad Halsey | Arizona Diamondbacks | Oakland Athletics | Trade |
| Mar 26, 2006 | Trade | Juan Cruz | Oakland Athletics | Arizona Diamondbacks | Trade |
| Mar 25, 2006 | Signed as free agent | Alex Sanchez | — | Cincinnati Reds | Free agent signing |
| Mar 25, 2006 | Released | Andy Van Hekken | Florida Marlins | — | Release |
| Mar 24, 2006 | Released | Felix Heredia | Arizona Diamondbacks | — | Release |
| Mar 24, 2006 | Signed as free agent | Michel Hernandez | — | St. Louis Cardinals | Free agent signing |
| Mar 24, 2006 | Released | Blaine Neal | St. Louis Cardinals | — | Release |
| Mar 23, 2006 | Released | Brian Boehringer | Chicago Cubs | — | Release |
| Mar 23, 2006 | Released | Valerio De Los Santos | Washington Nationals | — | Release |
| Mar 23, 2006 | Released | Mike Difelice | Washington Nationals | — | Release |
| Mar 23, 2006 | Released | David Lee | Chicago Cubs | — | Release |
| Mar 23, 2006 | Signed as free agent | Billy Traber | — | Washington Nationals | Free agent signing |
| Mar 22, 2006 | Released | Dave Berg | St. Louis Cardinals | — | Release |
| Mar 22, 2006 | Released | Ricky Bottalico | Baltimore Orioles | — | Release |
| Mar 21, 2006 | Trade | Bobby Basham | Cincinnati Reds | San Diego Padres | Trade |
| Mar 21, 2006 | Trade | David Ross | San Diego Padres | Cincinnati Reds | Trade |
| Mar 20, 2006 | Released | Graham Koonce | New York Yankees | — | Release |
| Mar 20, 2006 | Signed as free agent | Jorge Padilla | — | New York Mets | Free agent signing |
| Mar 20, 2006 | Signed as free agent | Mark Quinn | — | Chicago White Sox | Free agent signing |
| Mar 20, 2006 | Trade | Joe Borchard | Chicago White Sox | Seattle Mariners | Trade |
| Mar 20, 2006 | Trade | Matt Thornton | Seattle Mariners | Chicago White Sox | Trade |
| Mar 20, 2006 | Trade | Unnamed | Boston Red Sox | Cincinnati Reds | $ |
| Mar 20, 2006 | Trade | Bronson Arroyo | Boston Red Sox | Cincinnati Reds | Trade |
| Mar 20, 2006 | Trade | Wily Mo Peña | Cincinnati Reds | Boston Red Sox | Trade |
| Mar 19, 2006 | Released | Frank Brooks | New York Yankees | — | Release |
| Mar 19, 2006 | Signed as free agent | Bernie Castro | — | Washington Nationals | Free agent signing |
| Mar 19, 2006 | Signed as free agent | Juan Gonzalez | — | Boston Red Sox | Free agent signing |
| Mar 19, 2006 | Signed as free agent | Damian Moss | — | Atlanta Braves | Free agent signing |
| Mar 19, 2006 | Signed as free agent | Alberto Reyes | — | Tampa Bay Devil Rays | Free agent signing |
| Mar 19, 2006 | Released | Karl Rhodes | Cincinnati Reds | — | Release |
| Mar 19, 2006 | Signed as free agent | Allan Simpson | — | Milwaukee Brewers | Free agent signing |
| Mar 19, 2006 | Signed | Joel De La Cruz | — | Milwaukee Brewers | Amateur free agent signing |
| Mar 16, 2006 | Signed as free agent | Javier Cardona | — | Boston Red Sox | Free agent signing |
| Mar 15, 2006 | Released | Allan Simpson | Cincinnati Reds | — | Release |
| Mar 13, 2006 | Signed as free agent | Luke Hudson | — | Kansas City Royals | Free agent signing |
| Mar 11, 2006 | Signed as free agent | Raul Gonzalez | — | Pittsburgh Pirates | Free agent signing |
| Mar 10, 2006 | Signed as free agent | Peter Moylan | — | Atlanta Braves | Free agent signing |
| Mar 9, 2006 | Released | Luke Hudson | Cincinnati Reds | — | Release |
| Mar 8, 2006 | Signed as free agent | Dave Coggin | — | Atlanta Braves | Free agent signing |
| Mar 8, 2006 | Trade | Alex Cintron | Arizona Diamondbacks | Chicago White Sox | Trade |
| Mar 8, 2006 | Trade | Jeff Bajenaru | Chicago White Sox | Arizona Diamondbacks | Trade |
| Mar 7, 2006 | Signed as free agent | Craig Brazell | — | Los Angeles Dodgers | Free agent signing |
| Mar 6, 2006 | Signed as free agent | Hideo Nomo | — | Chicago White Sox | Free agent signing |
| Mar 6, 2006 | Signed as free agent | Vladimir Nunez | — | Chicago White Sox | Free agent signing |
| Mar 5, 2006 | Signed | Greg Burke | — | San Diego Padres | Amateur free agent signing |
| Mar 5, 2006 | Signed as free agent | Jeff Farnsworth | — | Chicago White Sox | Free agent signing |
| Mar 5, 2006 | Released | Ryan Jensen | Baltimore Orioles | — | Release |
| Mar 5, 2006 | Released | Pokey Reese | Florida Marlins | — | Release |
| Mar 4, 2006 | Signed as free agent | Brian Bowles | — | Baltimore Orioles | Free agent signing |
| Mar 4, 2006 | Signed as free agent | Dee Brown | — | Kansas City Royals | Free agent signing |
| Mar 3, 2006 | Signed as free agent | Ruben Rivera | — | Chicago White Sox | Free agent signing |
| Mar 2, 2006 | Signed as free agent | Jose Acevedo | — | Colorado Rockies | Free agent signing |
| Mar 2, 2006 | Signed as free agent | Pedro Astacio | — | Washington Nationals | Free agent signing |
| Mar 2, 2006 | Released | Ryan Glynn | Minnesota Twins | — | Release |
| Mar 2, 2006 | Released | Tim Raines | Minnesota Twins | — | Release |
| Mar 2, 2006 | Signed as free agent | Mark Watson | — | Chicago Cubs | Free agent signing |
| Mar 1, 2006 | Signed as free agent | Willie Collazo | — | New York Mets | Free agent signing |
| Mar 1, 2006 | Signed as free agent | Alex Gonzalez | — | Philadelphia Phillies | Free agent signing |
| Feb 28, 2006 | Signed as free agent | Pedro Feliciano | — | New York Mets | Free agent signing |
| Feb 28, 2006 | Trade | Alberto Callaspo | Los Angeles Angels of Anaheim | Arizona Diamondbacks | Trade |
| Feb 28, 2006 | Trade | Jason Bulger | Arizona Diamondbacks | Los Angeles Angels of Anaheim | Trade |
| Feb 27, 2006 | Signed as free agent | Brian Boehringer | — | Chicago Cubs | Free agent signing |
| Feb 27, 2006 | Signed as free agent | Jason Romano | — | Milwaukee Brewers | Free agent signing |
| Feb 26, 2006 | Signed as free agent | Richard Hidalgo | — | Baltimore Orioles | Free agent signing |
| Feb 26, 2006 | Signed as free agent | Steve Lomasney | — | Minnesota Twins | Free agent signing |
| Feb 25, 2006 | Signed as free agent | Tom Wilson | — | Florida Marlins | Free agent signing |
| Feb 24, 2006 | Signed as free agent | Alex Escobar | — | Washington Nationals | Free agent signing |
| Feb 24, 2006 | Released | Ramon Nivar | St. Louis Cardinals | — | Release |
| Feb 23, 2006 | Signed as free agent | Jeff Weaver | — | Los Angeles Angels of Anaheim | Free agent signing |
| Feb 23, 2006 | Signed as free agent | Keiichi Yabu | — | Colorado Rockies | Free agent signing |
| Feb 22, 2006 | Signed as free agent | Bryan Corey | — | Chicago Cubs | Free agent signing |
| Feb 22, 2006 | Signed as free agent | Kevin Millwood | — | Texas Rangers | Free agent signing |
| Feb 22, 2006 | Signed as free agent | Roberto Petagine | — | Seattle Mariners | Free agent signing |
| Feb 21, 2006 | Signed as free agent | Erubiel Durazo | — | Texas Rangers | Free agent signing |
| Feb 21, 2006 | Signed as free agent | Josh Hancock | — | St. Louis Cardinals | Free agent signing |
| Feb 21, 2006 | Signed as free agent | Dennys Reyes | — | Minnesota Twins | Free agent signing |
| Feb 21, 2006 | Signed as free agent | Ryan Snare | — | Kansas City Royals | Free agent signing |
| Feb 21, 2006 | Signed as free agent | Ed Yarnall | — | Kansas City Royals | Free agent signing |
| Feb 20, 2006 | Signed as free agent | Brian Buchanan | — | Cincinnati Reds | Free agent signing |
| Feb 20, 2006 | Signed as free agent | Kevin Gryboski | — | Washington Nationals | Free agent signing |
| Feb 20, 2006 | Signed as free agent | Chris Michalak | — | Cincinnati Reds | Free agent signing |
| Feb 20, 2006 | Signed as free agent | Franklin Nunez | — | Boston Red Sox | Free agent signing |
| Feb 19, 2006 | Signed as free agent | Mike Difelice | — | Washington Nationals | Free agent signing |
| Feb 19, 2006 | Signed as free agent | Wes Obermueller | — | Atlanta Braves | Free agent signing |
| Feb 17, 2006 | Signed as free agent | Bobby Jones | — | Detroit Tigers | Free agent signing |
| Feb 17, 2006 | Signed as free agent | Scott Spiezio | — | St. Louis Cardinals | Free agent signing |
| Feb 16, 2006 | Signed as free agent | Carlos Almanzar | — | Atlanta Braves | Free agent signing |
| Feb 16, 2006 | Signed | Francisley Bueno | — | Atlanta Braves | Amateur free agent signing |
| Feb 16, 2006 | Signed as free agent | Scott Erickson | — | New York Yankees | Free agent signing |
| Feb 16, 2006 | Signed as free agent | Rob Sasser | — | Chicago White Sox | Free agent signing |
| Feb 16, 2006 | Signed | Jose Martinez | — | Chicago White Sox | Amateur free agent signing |
| Feb 14, 2006 | Signed as free agent | Scott Hatteberg | — | Cincinnati Reds | Free agent signing |
| Feb 14, 2006 | Signed as free agent | Jose Lima | — | New York Mets | Free agent signing |
| Feb 14, 2006 | Signed as free agent | Quinton McCracken | — | Cincinnati Reds | Free agent signing |
| Feb 14, 2006 | Signed as free agent | Karl Rhodes | — | Cincinnati Reds | Free agent signing |
| Feb 14, 2006 | Signed as free agent | Brandon Villafuerte | — | San Francisco Giants | Free agent signing |
| Feb 14, 2006 | Signed | Josmil Pinto | — | Minnesota Twins | Amateur free agent signing |
| Feb 13, 2006 | Signed | Wilin Rosario | — | Colorado Rockies | Amateur free agent signing |
| Feb 11, 2006 | Signed as free agent | Travis Lee | — | Tampa Bay Devil Rays | Free agent signing |
| Feb 10, 2006 | Signed as free agent | Josh Fogg | — | Colorado Rockies | Free agent signing |
| Feb 10, 2006 | Signed as free agent | Todd Greene | — | San Francisco Giants | Free agent signing |
| Feb 10, 2006 | Signed as free agent | Felix Heredia | — | Arizona Diamondbacks | Free agent signing |
| Feb 10, 2006 | Signed as free agent | Graham Koonce | — | New York Yankees | Free agent signing |
| Feb 10, 2006 | Signed as free agent | Timo Perez | — | Cincinnati Reds | Free agent signing |
| Feb 10, 2006 | Signed as free agent | Santiago Ramirez | — | Washington Nationals | Free agent signing |
| Feb 9, 2006 | Signed as free agent | Mike Bacsik | — | Washington Nationals | Free agent signing |
| Feb 9, 2006 | Signed as free agent | Jim Crowell | — | Washington Nationals | Free agent signing |
| Feb 9, 2006 | Signed as free agent | Brandon Larson | — | Washington Nationals | Free agent signing |
| Feb 8, 2006 | Signed as free agent | Antonio Alfonseca | — | Texas Rangers | Free agent signing |
| Feb 8, 2006 | Signed as free agent | Vic Darensbourg | — | Baltimore Orioles | Free agent signing |
| Feb 8, 2006 | Signed as free agent | Matt Duff | — | Toronto Blue Jays | Free agent signing |
| Feb 8, 2006 | Signed as free agent | Matt Erickson | — | Arizona Diamondbacks | Free agent signing |
| Feb 8, 2006 | Signed as free agent | Brian Esposito | — | St. Louis Cardinals | Free agent signing |
| Feb 8, 2006 | Signed as free agent | John Halama | — | Baltimore Orioles | Free agent signing |
| Feb 8, 2006 | Signed as free agent | Bo Hart | — | Colorado Rockies | Free agent signing |
| Feb 8, 2006 | Signed as free agent | Ryan Jensen | — | Baltimore Orioles | Free agent signing |
| Feb 8, 2006 | Signed as free agent | Matt LeCroy | — | Washington Nationals | Free agent signing |
| Feb 8, 2006 | Signed as free agent | Juan Melo | — | Colorado Rockies | Free agent signing |
| Feb 8, 2006 | Signed as free agent | Desi Relaford | — | Baltimore Orioles | Free agent signing |
| Feb 7, 2006 | Signed as free agent | Brian Anderson | — | Texas Rangers | Free agent signing |
| Feb 7, 2006 | Signed as free agent | Jeff DaVanon | — | Arizona Diamondbacks | Free agent signing |
| Feb 7, 2006 | Signed as free agent | Takashi Saito | — | Los Angeles Dodgers | Free agent signing with first major-league team |
| Feb 6, 2006 | Signed as free agent | Jimmy Anderson | — | Florida Marlins | Free agent signing |
| Feb 6, 2006 | Signed as free agent | Cha-Seung Baek | — | Seattle Mariners | Free agent signing |
| Feb 6, 2006 | Signed as free agent | John Ennis | — | Chicago Cubs | Free agent signing |
| Feb 6, 2006 | Signed as free agent | Eddie Gaillard | — | Florida Marlins | Free agent signing |
| Feb 6, 2006 | Signed as free agent | Alex Gonzalez | — | Boston Red Sox | Free agent signing |
| Feb 6, 2006 | Signed as free agent | Anastacio Martinez | — | Washington Nationals | Free agent signing |
| Feb 6, 2006 | Signed as free agent | Brian Meadows | — | Los Angeles Dodgers | Free agent signing |
| Feb 6, 2006 | Signed as free agent | Bengie Molina | — | Toronto Blue Jays | Free agent signing |
| Feb 6, 2006 | Released | Roberto Petagine | Boston Red Sox | — | Release |
| Feb 6, 2006 | Signed as free agent | Mike Vento | — | Washington Nationals | Free agent signing |
| Feb 4, 2006 | Signed as free agent | Kurt Ainsworth | — | Los Angeles Dodgers | Free agent signing |
| Feb 4, 2006 | Signed as free agent | Ricky Bottalico | — | Baltimore Orioles | Free agent signing |
| Feb 4, 2006 | Signed as free agent | Craig Breslow | — | Boston Red Sox | Free agent signing |
| Feb 4, 2006 | Signed | Barbaro Canizares | — | Atlanta Braves | Amateur free agent signing |
| Feb 3, 2006 | Released | Todd Greene | San Diego Padres | — | Release |
| Feb 3, 2006 | Signed as free agent | Mike Piazza | — | San Diego Padres | Free agent signing |
| Feb 2, 2006 | Signed as free agent | Royce Clayton | — | Washington Nationals | Free agent signing |
| Feb 2, 2006 | Signed as free agent | Brandon Knight | — | Pittsburgh Pirates | Free agent signing |
| Feb 2, 2006 | Signed as free agent | George Lombard | — | Washington Nationals | Free agent signing |
| Feb 2, 2006 | Released | Todd Ritchie | Pittsburgh Pirates | — | Release |
| Feb 1, 2006 | Signed as free agent | Chad Allen | — | Kansas City Royals | Free agent signing |
| Feb 1, 2006 | Signed as free agent | Pat Borders | — | Los Angeles Dodgers | Free agent signing |
| Feb 1, 2006 | Signed as free agent | Ron Calloway | — | Boston Red Sox | Free agent signing |
| Feb 1, 2006 | Signed as free agent | Jermaine Clark | — | Milwaukee Brewers | Free agent signing |
| Feb 1, 2006 | Signed as free agent | Trent Durrington | — | Boston Red Sox | Free agent signing |
| Feb 1, 2006 | Signed as free agent | Matt Ginter | — | Boston Red Sox | Free agent signing |
| Feb 1, 2006 | Signed as free agent | Mike Holtz | — | Boston Red Sox | Free agent signing |
| Feb 1, 2006 | Signed as free agent | Ken Huckaby | — | Boston Red Sox | Free agent signing |
| Feb 1, 2006 | Signed as free agent | Luis Jimenez | — | Boston Red Sox | Free agent signing |
| Feb 1, 2006 | Signed as free agent | Bobby Keppel | — | Kansas City Royals | Free agent signing |
| Feb 1, 2006 | Signed as free agent | Dustan Mohr | — | Boston Red Sox | Free agent signing |
| Feb 1, 2006 | Signed as free agent | Rick White | — | Cincinnati Reds | Free agent signing |
| Feb 1, 2006 | Signed as free agent | Enrique Wilson | — | Boston Red Sox | Free agent signing |
| Jan 31, 2006 | Signed as free agent | Russell Branyan | — | Tampa Bay Devil Rays | Free agent signing |
| Jan 31, 2006 | Signed as free agent | Jim Brower | — | Baltimore Orioles | Free agent signing |
| Jan 31, 2006 | Signed as free agent | Ryan Glynn | — | Minnesota Twins | Free agent signing |
| Jan 31, 2006 | Signed as free agent | Luther Hackman | — | St. Louis Cardinals | Free agent signing |
| Jan 31, 2006 | Signed as free agent | Ramon Martinez | — | Los Angeles Dodgers | Free agent signing |
| Jan 31, 2006 | Signed as free agent | Peter Munro | — | Minnesota Twins | Free agent signing |
| Jan 31, 2006 | Signed as free agent | Tim Raines | — | Minnesota Twins | Free agent signing |
| Jan 31, 2006 | Signed as free agent | Felix Rodriguez | — | Washington Nationals | Free agent signing |
| Jan 31, 2006 | Signed as free agent | Ruben Sierra | — | Minnesota Twins | Free agent signing |
| Jan 31, 2006 | Signed as free agent | Jamal Strong | — | Chicago Cubs | Free agent signing |
| Jan 31, 2006 | Signed as free agent | Frank Thomas | — | Oakland Athletics | Free agent signing |
| Jan 30, 2006 | Signed as free agent | James Baldwin | — | Toronto Blue Jays | Free agent signing |
| Jan 30, 2006 | Signed as free agent | Jeff Duncan | — | Los Angeles Dodgers | Free agent signing |
| Jan 30, 2006 | Signed as free agent | Ramiro Mendoza | — | New York Yankees | Free agent signing |
| Jan 30, 2006 | Signed as free agent | Neal Musser | — | Arizona Diamondbacks | Free agent signing |
| Jan 29, 2006 | Signed as free agent | Joe Winkelsas | — | Milwaukee Brewers | Free agent signing |
| Jan 28, 2006 | Signed | Eduardo Escobar | — | Chicago White Sox | Amateur free agent signing |
| Jan 28, 2006 | Signed as free agent | Joe Thurston | — | Philadelphia Phillies | Free agent signing |
| Jan 28, 2006 | Signed as free agent | Ben Weber | — | Toronto Blue Jays | Free agent signing |
| Jan 27, 2006 | Signed as free agent | Valerio De Los Santos | — | Washington Nationals | Free agent signing |
| Jan 27, 2006 | Signed as free agent | Ken Harvey | — | Kansas City Royals | Free agent signing |
| Jan 27, 2006 | Signed as free agent | Jose Hernandez | — | Pittsburgh Pirates | Free agent signing |
| Jan 27, 2006 | Signed as free agent | Henry Mateo | — | Washington Nationals | Free agent signing |
| Jan 27, 2006 | Signed as free agent | Daryle Ward | — | Washington Nationals | Free agent signing |
| Jan 27, 2006 | Trade | Unnamed | Boston Red Sox | Cleveland Indians | $ |
| Jan 27, 2006 | Trade | Guillermo Mota | Boston Red Sox | Cleveland Indians | Trade |
| Jan 27, 2006 | Trade | Andy Marte | Boston Red Sox | Cleveland Indians | Trade |
| Jan 27, 2006 | Trade | Kelly Shoppach | Boston Red Sox | Cleveland Indians | Trade |
| Jan 27, 2006 | Trade | Coco Crisp | Cleveland Indians | Boston Red Sox | Trade |
| Jan 27, 2006 | Trade | David Riske | Cleveland Indians | Boston Red Sox | Trade |
| Jan 27, 2006 | Trade | Josh Bard | Cleveland Indians | Boston Red Sox | Trade |
| Jan 27, 2006 | Trade | Arthur Rhodes | Cleveland Indians | Philadelphia Phillies | Trade |
| Jan 27, 2006 | Trade | Jason Michaels | Philadelphia Phillies | Cleveland Indians | Trade |
| Jan 26, 2006 | Signed as free agent | J. R. House | — | Houston Astros | Free agent signing |
| Jan 26, 2006 | Signed as free agent | Damian Rolls | — | New York Yankees | Free agent signing |
| Jan 26, 2006 | Signed as free agent | Wilkin Ruan | — | Los Angeles Dodgers | Free agent signing |
| Jan 26, 2006 | Signed as free agent | Jared Sandberg | — | Houston Astros | Free agent signing |
| Jan 25, 2006 | Signed as free agent | Miguel Asencio | — | Colorado Rockies | Free agent signing |
| Jan 25, 2006 | Signed as free agent | Mike Remlinger | — | Atlanta Braves | Free agent signing |
| Jan 25, 2006 | Signed as free agent | Jose Silva | — | Texas Rangers | Free agent signing |
| Jan 25, 2006 | Signed as free agent | Rico Washington | — | St. Louis Cardinals | Free agent signing |
| Jan 24, 2006 | Signed as free agent | Joe Beimel | — | Los Angeles Dodgers | Free agent signing |
| Jan 24, 2006 | Signed as free agent | Wayne Franklin | — | Tampa Bay Devil Rays | Free agent signing |
| Jan 24, 2006 | Signed as free agent | Geremi Gonzalez | — | New York Mets | Free agent signing |
| Jan 24, 2006 | Signed as free agent | Wiki Gonzalez | — | Washington Nationals | Free agent signing |
| Jan 24, 2006 | Signed as free agent | Matt Herges | — | Florida Marlins | Free agent signing |
| Jan 24, 2006 | Signed as free agent | Steve Kent | — | Houston Astros | Free agent signing |
| Jan 24, 2006 | Signed as free agent | Esix Snead | — | Baltimore Orioles | Free agent signing |
| Jan 24, 2006 | Signed as free agent | Tyler Yates | — | Baltimore Orioles | Free agent signing |
| Jan 23, 2006 | Signed as free agent | Jon Adkins | — | San Diego Padres | Free agent signing |
| Jan 23, 2006 | Signed as free agent | Gabe Kapler | — | Boston Red Sox | Free agent signing |
| Jan 23, 2006 | Signed as free agent | Wade Miller | — | Chicago Cubs | Free agent signing |
| Jan 22, 2006 | Trade | Kris Benson | New York Mets | Baltimore Orioles | Trade |
| Jan 22, 2006 | Trade | Jorge Julio | Baltimore Orioles | New York Mets | Trade |
| Jan 22, 2006 | Trade | John Maine | Baltimore Orioles | New York Mets | Trade |
| Jan 21, 2006 | Signed as free agent | Mike Venafro | — | New York Mets | Free agent signing |
| Jan 20, 2006 | Signed as free agent | Troy Cate | — | St. Louis Cardinals | Free agent signing |
| Jan 19, 2006 | Signed as free agent | Willie Harris | — | Boston Red Sox | Free agent signing |
| Jan 19, 2006 | Signed as free agent | Ruben Mateo | — | Washington Nationals | Free agent signing |
| Jan 19, 2006 | Signed as free agent | Agustin Montero | — | Chicago White Sox | Free agent signing |
| Jan 19, 2006 | Signed as free agent | Darren Oliver | — | New York Mets | Free agent signing |
| Jan 19, 2006 | Signed as free agent | Randy Ruiz | — | Kansas City Royals | Free agent signing |
| Jan 19, 2006 | Signed as free agent | Matt Skrmetta | — | Chicago Cubs | Free agent signing |
| Jan 19, 2006 | Signed as free agent | Jorge Velandia | — | Chicago White Sox | Free agent signing |
| Jan 19, 2006 | Signed as free agent | Les Walrond | — | Chicago Cubs | Free agent signing |
| Jan 18, 2006 | Signed as free agent | Terry Adams | — | Pittsburgh Pirates | Free agent signing |
| Jan 18, 2006 | Signed as free agent | Melvin Dorta | — | Washington Nationals | Free agent signing |
| Jan 18, 2006 | Signed as free agent | Tom Gregorio | — | Seattle Mariners | Free agent signing |
| Jan 18, 2006 | Signed as free agent | Brian Jordan | — | Atlanta Braves | Free agent signing |
| Jan 18, 2006 | Signed as free agent | Tom Martin | — | Colorado Rockies | Free agent signing |
| Jan 18, 2006 | Signed as free agent | Luis Rivas | — | Tampa Bay Devil Rays | Free agent signing |
| Jan 18, 2006 | Signed as free agent | Carlos Rivera | — | Colorado Rockies | Free agent signing |
| Jan 18, 2006 | Signed as free agent | Julian Tavarez | — | Boston Red Sox | Free agent signing |
| Jan 18, 2006 | Signed as free agent | Jorge Vasquez | — | Pittsburgh Pirates | Free agent signing |
| Jan 17, 2006 | Signed as free agent | Tony Alvarez | — | Baltimore Orioles | Free agent signing |
| Jan 17, 2006 | Signed as free agent | Matt Anderson | — | San Francisco Giants | Free agent signing |
| Jan 17, 2006 | Signed as free agent | Shawn Camp | — | Tampa Bay Devil Rays | Free agent signing |
| Jan 17, 2006 | Released | Mike Cervenak | San Francisco Giants | — | Release |
| Jan 17, 2006 | Signed as free agent | Pedro Liriano | — | San Francisco Giants | Free agent signing |
| Jan 17, 2006 | Signed as free agent | Abraham Nunez | — | San Francisco Giants | Free agent signing |
| Jan 17, 2006 | Signed as free agent | Donnie Sadler | — | Arizona Diamondbacks | Free agent signing |
| Jan 17, 2006 | Signed as free agent | Michael Tejera | — | San Francisco Giants | Free agent signing |
| Jan 17, 2006 | Signed as free agent | Jamey Wright | — | San Francisco Giants | Free agent signing |
| Jan 17, 2006 | Trade | Brian Tallet | Cleveland Indians | Toronto Blue Jays | Trade |
| Jan 17, 2006 | Trade | Bubbie Buzachero | Toronto Blue Jays | Cleveland Indians | Trade |
| Jan 16, 2006 | Signed as free agent | Jeremy Hill | — | New York Mets | Free agent signing |
| Jan 16, 2006 | Signed as free agent | Jeff Nelson | — | St. Louis Cardinals | Free agent signing |
| Jan 15, 2006 | Signed as free agent | Mike Rose | — | Tampa Bay Devil Rays | Free agent signing |
| Jan 15, 2006 | Signed as free agent | Scott Seabol | — | Florida Marlins | Free agent signing |
| Jan 14, 2006 | Signed as free agent | Pascual Matos | — | Chicago White Sox | Free agent signing |
| Jan 14, 2006 | Signed as free agent | Aaron Sele | — | Los Angeles Dodgers | Free agent signing |
| Jan 14, 2006 | Trade | Danys Baez | Tampa Bay Devil Rays | Los Angeles Dodgers | Trade |
| Jan 14, 2006 | Trade | Lance Carter | Tampa Bay Devil Rays | Los Angeles Dodgers | Trade |
| Jan 14, 2006 | Trade | Edwin Jackson | Los Angeles Dodgers | Tampa Bay Devil Rays | Trade |
| Jan 14, 2006 | Trade | Chuck Tiffany | Los Angeles Dodgers | Tampa Bay Devil Rays | Trade |
| Jan 13, 2006 | Signed as free agent | Michael Coleman | — | Tampa Bay Devil Rays | Free agent signing |
| Jan 13, 2006 | Signed as free agent | Ryan Franklin | — | Philadelphia Phillies | Free agent signing |
| Jan 13, 2006 | Signed as free agent | Kevin Millar | — | Baltimore Orioles | Free agent signing |
| Jan 13, 2006 | Signed as free agent | Eduardo Perez | — | Cleveland Indians | Free agent signing |
| Jan 13, 2006 | Signed as free agent | Eddy Rodriguez | — | Baltimore Orioles | Free agent signing |
| Jan 12, 2006 | Signed as free agent | Grant Balfour | — | Cincinnati Reds | Free agent signing |
| Jan 12, 2006 | Signed as free agent | Micah Bowie | — | Washington Nationals | Free agent signing |
| Jan 12, 2006 | Signed as free agent | Alan Embree | — | San Diego Padres | Free agent signing |
| Jan 12, 2006 | Signed as free agent | Andrew Good | — | Washington Nationals | Free agent signing |
| Jan 12, 2006 | Released | Josh Hancock | Cincinnati Reds | — | Release |
| Jan 12, 2006 | Signed as free agent | Paul Hoover | — | Florida Marlins | Free agent signing |
| Jan 12, 2006 | Signed as free agent | Matt Kinney | — | San Francisco Giants | Free agent signing |
| Jan 12, 2006 | Signed as free agent | Justin Leone | — | San Diego Padres | Free agent signing |
| Jan 12, 2006 | Signed as free agent | Frank Menechino | — | Cincinnati Reds | Free agent signing |
| Jan 12, 2006 | Signed as free agent | Terry Mulholland | — | Arizona Diamondbacks | Free agent signing |
| Jan 12, 2006 | Signed as free agent | Reggie Taylor | — | Detroit Tigers | Free agent signing |
| Jan 12, 2006 | Signed as free agent | Eric Valent | — | San Diego Padres | Free agent signing |
| Jan 11, 2006 | Signed as free agent | Matt Blank | — | Toronto Blue Jays | Free agent signing |
| Jan 11, 2006 | Signed as free agent | Jason Childers | — | Tampa Bay Devil Rays | Free agent signing |
| Jan 11, 2006 | Signed as free agent | Jeff Conine | — | Baltimore Orioles | Free agent signing |
| Jan 11, 2006 | Signed as free agent | Shawn Estes | — | San Diego Padres | Free agent signing |
| Jan 11, 2006 | Signed as free agent | Tony Graffanino | — | Boston Red Sox | Free agent signing |
| Jan 11, 2006 | Signed as free agent | Matt Lawton | — | Seattle Mariners | Free agent signing |
| Jan 11, 2006 | Signed as free agent | Mike Mahoney | — | Toronto Blue Jays | Free agent signing |
| Jan 11, 2006 | Signed as free agent | Mark Malaska | — | Tampa Bay Devil Rays | Free agent signing |
| Jan 11, 2006 | Signed as free agent | Dan Miceli | — | Tampa Bay Devil Rays | Free agent signing |
| Jan 11, 2006 | Signed as free agent | Justin Miller | — | Tampa Bay Devil Rays | Free agent signing |
| Jan 11, 2006 | Signed as free agent | Greg Norton | — | Tampa Bay Devil Rays | Free agent signing |
| Jan 11, 2006 | Released | Franklin Nunez | Tampa Bay Devil Rays | — | Release |
| Jan 11, 2006 | Signed as free agent | Phil Stockman | — | Atlanta Braves | Free agent signing |
| Jan 11, 2006 | Signed as free agent | Corey Thurman | — | Milwaukee Brewers | Free agent signing |
| Jan 11, 2006 | Signed as free agent | Michael Tucker | — | Washington Nationals | Free agent signing |
| Jan 11, 2006 | Signed as free agent | Joe Valentine | — | Houston Astros | Free agent signing |
| Jan 11, 2006 | Signed as free agent | Kevin Witt | — | Tampa Bay Devil Rays | Free agent signing |
| Jan 11, 2006 | Signed as free agent | Kelly Wunsch | — | Los Angeles Dodgers | Free agent signing |
| Jan 10, 2006 | Signed as free agent | Cesar Crespo | — | Atlanta Braves | Free agent signing |
| Jan 10, 2006 | Signed as free agent | Juan Encarnacion | — | St. Louis Cardinals | Free agent signing |
| Jan 10, 2006 | Signed as free agent | Lee Gardner | — | Detroit Tigers | Free agent signing |
| Jan 10, 2006 | Signed as free agent | Jacque Jones | — | Chicago Cubs | Free agent signing |
| Jan 10, 2006 | Signed as free agent | Matt Mantei | — | Detroit Tigers | Free agent signing |
| Jan 10, 2006 | Signed as free agent | Trever Miller | — | Houston Astros | Free agent signing |
| Jan 10, 2006 | Signed as free agent | Tim Olson | — | Texas Rangers | Free agent signing |
| Jan 10, 2006 | Signed as free agent | Josh Phelps | — | Detroit Tigers | Free agent signing |
| Jan 10, 2006 | Signed as free agent | Jason Phillips | — | Toronto Blue Jays | Free agent signing |
| Jan 10, 2006 | Signed as free agent | Mike Ryan | — | Atlanta Braves | Free agent signing |
| Jan 10, 2006 | Signed as free agent | Chris Saenz | — | Milwaukee Brewers | Free agent signing |
| Jan 10, 2006 | Signed as free agent | Bobby Scales | — | Philadelphia Phillies | Free agent signing |
| Jan 10, 2006 | Signed as free agent | Todd Sears | — | Seattle Mariners | Free agent signing |
| Jan 10, 2006 | Signed as free agent | Travis Smith | — | Atlanta Braves | Free agent signing |
| Jan 10, 2006 | Signed as free agent | Dusty Wathan | — | Philadelphia Phillies | Free agent signing |
| Jan 10, 2006 | Signed as free agent | Matt White | — | Philadelphia Phillies | Free agent signing |
| Jan 10, 2006 | Signed as free agent | Ty Wigginton | — | Tampa Bay Devil Rays | Free agent signing |
| Jan 9, 2006 | Signed as free agent | Kevin Appier | — | Seattle Mariners | Free agent signing |
| Jan 9, 2006 | Signed as free agent | Jeromy Burnitz | — | Pittsburgh Pirates | Free agent signing |
| Jan 9, 2006 | Signed as free agent | Javier Lopez | — | Chicago White Sox | Free agent signing |
| Jan 9, 2006 | Signed as free agent | Darrell May | — | Minnesota Twins | Free agent signing |
| Jan 9, 2006 | Signed as free agent | Blaine Neal | — | St. Louis Cardinals | Free agent signing |
| Jan 9, 2006 | Signed as free agent | Steve Randolph | — | Chicago White Sox | Free agent signing |
| Jan 9, 2006 | Signed as free agent | Cody Ransom | — | Seattle Mariners | Free agent signing |
| Jan 9, 2006 | Signed as free agent | J. T. Snow | — | Boston Red Sox | Free agent signing |
| Jan 9, 2006 | Signed as free agent | Alan Zinter | — | Houston Astros | Free agent signing |
| Jan 9, 2006 | Trade | Nate Spears | Baltimore Orioles | Chicago Cubs | Trade |
| Jan 9, 2006 | Trade | Carlos Perez | Baltimore Orioles | Chicago Cubs | Trade |
| Jan 9, 2006 | Trade | Corey Patterson | Chicago Cubs | Baltimore Orioles | Trade |
| Jan 8, 2006 | Signed as free agent | Rich Aurilia | — | Cincinnati Reds | Free agent signing |
| Jan 7, 2006 | Signed as free agent | Byung-Hyun Kim | — | Colorado Rockies | Free agent signing |
| Jan 7, 2006 | Signed as free agent | Eli Marrero | — | Colorado Rockies | Free agent signing |
| Jan 6, 2006 | Released | Russell Branyan | Milwaukee Brewers | — | Release |
| Jan 6, 2006 | Signed as free agent | Frank Brooks | — | New York Yankees | Free agent signing |
| Jan 6, 2006 | Signed as free agent | Miguel Cairo | — | New York Yankees | Free agent signing |
| Jan 6, 2006 | Signed as free agent | Mark Corey | — | New York Yankees | Free agent signing |
| Jan 6, 2006 | Signed as free agent | Ben Davis | — | New York Yankees | Free agent signing |
| Jan 6, 2006 | Signed as free agent | Adam Greenberg | — | Chicago Cubs | Free agent signing |
| Jan 6, 2006 | Signed as free agent | Todd Hollandsworth | — | Cleveland Indians | Free agent signing |
| Jan 6, 2006 | Signed as free agent | Al Leiter | — | New York Yankees | Free agent signing |
| Jan 6, 2006 | Signed as free agent | Eddie Perez | — | Atlanta Braves | Free agent signing |
| Jan 6, 2006 | Signed as free agent | Reggie Sanders | — | Kansas City Royals | Free agent signing |
| Jan 6, 2006 | Signed as free agent | Preston Wilson | — | Houston Astros | Free agent signing |
| Jan 6, 2006 | Trade | Corey Koskie | Toronto Blue Jays | Milwaukee Brewers | Trade |
| Jan 6, 2006 | Trade | Brian Wolfe | Milwaukee Brewers | Toronto Blue Jays | Trade |
| Jan 6, 2006 | Trade | Adam Eaton | San Diego Padres | Texas Rangers | Trade |
| Jan 6, 2006 | Trade | Akinori Otsuka | San Diego Padres | Texas Rangers | Trade |
| Jan 6, 2006 | Trade | Billy Killian | San Diego Padres | Texas Rangers | Trade |
| Jan 6, 2006 | Trade | Adrian Gonzalez | Texas Rangers | San Diego Padres | Trade |
| Jan 6, 2006 | Trade | Terrmel Sledge | Texas Rangers | San Diego Padres | Trade |
| Jan 6, 2006 | Trade | Chris Young | Texas Rangers | San Diego Padres | Trade |
| Jan 5, 2006 | Signed as free agent | Hiram Bocachica | — | Oakland Athletics | Free agent signing |
| Jan 5, 2006 | Signed as free agent | Raul Casanova | — | Oakland Athletics | Free agent signing |
| Jan 5, 2006 | Signed as free agent | Brandon Duckworth | — | Pittsburgh Pirates | Free agent signing |
| Jan 5, 2006 | Signed as free agent | Todd Greene | — | San Diego Padres | Free agent signing |
| Jan 5, 2006 | Signed as free agent | Randy Keisler | — | Oakland Athletics | Free agent signing |
| Jan 5, 2006 | Signed as free agent | Dave Matranga | — | San Diego Padres | Free agent signing |
| Jan 5, 2006 | Signed as free agent | Marty McLeary | — | Pittsburgh Pirates | Free agent signing |
| Jan 5, 2006 | Signed as free agent | C. J. Nitkowski | — | Pittsburgh Pirates | Free agent signing |
| Jan 5, 2006 | Signed as free agent | Junior Spivey | — | St. Louis Cardinals | Free agent signing |
| Jan 4, 2006 | Signed as free agent | Octavio Dotel | — | New York Yankees | Free agent signing |
| Jan 4, 2006 | Signed as free agent | Carl Everett | — | Seattle Mariners | Free agent signing |
| Jan 4, 2006 | Signed as free agent | Danny Kolb | — | Milwaukee Brewers | Free agent signing |
| Jan 4, 2006 | Signed as free agent | Darnell McDonald | — | Tampa Bay Devil Rays | Free agent signing |
| Jan 4, 2006 | Signed as free agent | Hector Mercado | — | Detroit Tigers | Free agent signing |
| Jan 4, 2006 | Signed as free agent | Ramon Santiago | — | Detroit Tigers | Free agent signing |
| Jan 4, 2006 | Trade | Jae Weong Seo | New York Mets | Los Angeles Dodgers | Trade |
| Jan 4, 2006 | Trade | Tim Hamulack | New York Mets | Los Angeles Dodgers | Trade |
| Jan 4, 2006 | Trade | Duaner Sanchez | Los Angeles Dodgers | New York Mets | Trade |
| Jan 4, 2006 | Trade | Steve Schmoll | Los Angeles Dodgers | New York Mets | Trade |
| Jan 3, 2006 | Signed as free agent | Tony Armas | — | Washington Nationals | Free agent signing |
| Jan 3, 2006 | Signed as free agent | Joe Borowski | — | Florida Marlins | Free agent signing |
| Jan 3, 2006 | Signed as free agent | J. C. Boscan | — | Milwaukee Brewers | Free agent signing |
| Jan 3, 2006 | Signed as free agent | Johnny Damon | — | New York Yankees | Free agent signing |
| Jan 3, 2006 | Signed as free agent | Jose Diaz | — | Texas Rangers | Free agent signing |
| Jan 3, 2006 | Signed as free agent | John Flaherty | — | Boston Red Sox | Free agent signing |
| Jan 3, 2006 | Signed as free agent | Wes Helms | — | Florida Marlins | Free agent signing |
| Jan 3, 2006 | Signed as free agent | Jason Johnson | — | Cleveland Indians | Free agent signing |
| Jan 3, 2006 | Signed as free agent | Joe Mays | — | Kansas City Royals | Free agent signing |
| Jan 3, 2006 | Signed as free agent | Augie Ojeda | — | Chicago Cubs | Free agent signing |
| Jan 3, 2006 | Signed as free agent | Miguel Olivo | — | Florida Marlins | Free agent signing |
| Jan 3, 2006 | Signed as free agent | Joe Randa | — | Pittsburgh Pirates | Free agent signing |
| Jan 3, 2006 | Signed as free agent | Tim Redding | — | Chicago White Sox | Free agent signing |
| Jan 3, 2006 | Signed as free agent | Pokey Reese | — | Florida Marlins | Free agent signing |
| Jan 3, 2006 | Signed as free agent | Michael Restovich | — | Chicago Cubs | Free agent signing |
| Jan 3, 2006 | Signed as free agent | Brett Tomko | — | Los Angeles Dodgers | Free agent signing |
| Jan 3, 2006 | Signed as free agent | Jose Vizcaino | — | San Francisco Giants | Free agent signing |
| Jan 3, 2006 | Signed as free agent | Bernie Williams | — | New York Yankees | Free agent signing |
| Jan 2, 2006 | Signed as free agent | Lance Davis | — | Detroit Tigers | Free agent signing |
| Jan 2, 2006 | Signed as free agent | Scott Mullen | — | Atlanta Braves | Free agent signing |
| Jan 2, 2006 | Signed | Edgar Ibarra | — | Minnesota Twins | Amateur free agent signing |
| Jan 1, 2006 | Signed as free agent | Tony Fiore | — | Detroit Tigers | Free agent signing |
| Jan 1, 2006 | Signed as free agent | Justin Thompson | — | Milwaukee Brewers | Free agent signing |
Every row is mapped onto the same trade / signing / release vocabulary the modern feed uses, with the era’s own type description kept on each row. Club names are the names of the day (the Boston Braves years, the Brooklyn Dodgers years), and each links to the franchise it is today. Some dates are only partially known or flagged approximate by the source; they are shown exactly as published, never completed to a fake precise day.