| Team Transactions |
| DATE | TRANSACTION |
| December 19, 2006 | Agreed to terms with pitcher Masumi Kuwata on a minor-league contract. |
| December 19, 2006 | Signed pitcher Yoslan Herrera to a three-year contract. |
| December 15, 2006 | Signed pitchers John Wasdin, Kip Bouknight, Allan Simpson and Jim Brower, catcher David Parrish, infielders Eddy Garabito and Don Kelly and outfielders Michael Ryan and Chris Aguila to minor league contracts and invited them to spring training. |
| December 13, 2006 | Claimed pitcher Franquelis Osoria off waivers from the Los Angeles Dodgers. |
| November 1, 2006 | Named Roy Smith special assistant to the general manager and Tony Beasley minor league roving infield instructor. |
| October 14, 2006 | Purchased the contract of pitcher Josh Shortslef from Altoona of the Eastern League (AA). |
| October 12, 2006 | Promoted Joe Dellicarri to assistant scouting director; sent outright pitcher Mike Johnston to Indianapolis of the International League (AAA). |
| October 6, 2006 | Sent outright infielder Mike Edwards and pitcher Victor Santos to Indianapolis of the International League (AAA). |
| September 25, 2006 | Announced a four-year working agreement with the College Spikes of the New York Penn League (A). |
| September 7, 2006 | Recalled pitcher Juan Perez from Indianapolis of the International League (AAA); purchased the contracts of catcher Carlos Maldonado and pitcher Shane Youman from Indianapolis. |
| August 29, 2006 | Placed pitcher Mike Gonzalez on the 15-day disabled list, retroactive to Friday, with left elbow tendinitis; placed pitcher Tom Gorzelanny on the 15-day disabled list, retroactive to August 18, with left elbow tendinitis; designated pitcher Britt Reames for assignment; recalled pitcher Jonah Bayliss from Indianapolis of the International League (AAA); purchased the contracts of pitchers Marty McLeary and Brian Rogers from Indianapolis. |
| August 23, 2006 | Activated catcher Ryan Doumit from the 15-day disabled list; claimed pitcher Juan Perez off waivers from the New York Mets. |
| August 15, 2006 | Placed outfielder Nate McLouth on the 15-day disabled list with a sprained left ankle; recalled outfielder Rajai Davis from Indianapolis of the International League (AAA). |
| August 12, 2006 | Placed pitcher Josh Sharpless on the 15-day disabled list with a sprained right ankle; purchased the contract of pitcher Britt Reames from Indianapolis of the International League (AAA). |
| July 31, 2006 | Acquired minor league pitcher Brian Rogers from the Detroit Tigers for first baseman Sean Casey. |
| July 15, 2006 | Activated pitcher Victor Santos from the 15-day disabled list. |
| July 8, 2006 | Announced pitcher Ryan Vogelsong has cleared waivers and accepted an assignment to Indianapolis of the International League (AAA). |
| July 3, 2006 | Optioned infielder Mike Edwards to Indianapolis of the International League (AAA). |
| June 30, 2006 | Placed third baseman Joe Randa on the bereavement list; recalled infielder Mike Edwards from Indianapolis of the International League (AAA). |
| June 28, 2006 | Recalled pitcher Jonah Bayliss from Indianapolis of the International League (AAA); optioned pitcher Ryan Vogelsong to Indianapolis. |
| June 22, 2006 | Signed pitcher Brad Lincoln. |
| June 19, 2006 | Activated pitcher Kip Wells from the 15-day disabled list; placed pitcher Victor Santos on the 15-day disabled list with a strained right rotator cuff. |
| June 15, 2006 | Signed pitcher Michael Felix. |
| June 10, 2006 | Agreed to terms with pitchers Stephen MacFarland, Michael Crotta, Brandon Williams and Matthew McCullen, first basemen Kent Sakamoto and Gregory Smith, second baseman Jim Negrych, catcher Kris Watts, third baseman Jared Keel and outfielders Damian Walcott and Thomas Hagan. |
| June 6, 2006 | Placed catcher Ryan Doumit on the 15-day disabled list with a left hamstring strain; recalled infielder-outfielder Yurendell DeCaster from Indianapolis of the International League (AAA). |
| June 3, 2006 | Signed infielder Yurendall DeCaster to a one-year contract. |
| May 22, 2006 | Placed outfielder Jody Gerut on the 15-day disabled list. |
| May 22, 2006 | Placed infielder-outfielder Jose Bautista on the bereavement list; recalled infielder Yurendell DeCaster from Indianapolis of the International League (AAA). |
| May 18, 2006 | Placed outfielder Chris Duffy on the restricted list at Indianapolis of the International League (AAA) for not reporting to the club within the allotted 72-hour time period. |
| May 14, 2006 | Optioned outfielder Chris Duffy to Indianapolis of the International League (AAA); recalled infielder-outfielder Mike Edwards from Indianapolis. |
| May 7, 2006 | Recalled infielder Jose Bautista from Indianapolis of the International League (AAA); placed infielder Joe Randa on the 15-day disabled list, retroactive to Tuesday with a right foot bone contusion. |
| May 4, 2006 | Activated catcher Ryan Doumit from the 15-day disabled list; optioned infielder Mike Edwards to Indianapolis of the International League (AAA). |
| April 16, 2006 | Placed catcher Ryan Doumit on the 15-day disabled list, retroactive to Wednesday; recalled catcher Ronny Paulino from Indianapolis of the International League (AAA). |
| April 16, 2006 | Placed first baseman Sean Casey on the 15-day disabled list with two fractures of the transverse process in his left lower back; purchaed the contract of infielder-outfielder Mike Edwards from Indianapolis of the International League (AAA); transferred pitcher Kip Wells to the 60-day disabled list. |
| April 12, 2006 | Announced a two-year extension to working agreement with Indianapolis of the International League (AAA). |
| April 4, 2006 | Signed pitcher Salomon Torres to a two-year contract extension with a club option for the 2009 season. |
| April 4, 2006 | Signed general manager Dave Littlefield to a one-year contract extension through the 2008 season; signed pitcher Salomon Torres to a two-year contract extension with a club option for 2009. |
| March 31, 2006 | Optioned outfielder Jody Gerut to Indianapolis of the International League (AAA); assigned pitcher Brandon Duckworth to minor league camp; purchased the contract of infielder Jose Hernandez from Indianapolis; placed pitcher Bryan Bullington on the 60-day disabled list. |
| March 31, 2006 | Optioned outfielder Jody Gerut to Indianapolis of the International League; assigned pitcher Brandon Duckworth to minor league camp; purchased the contract of infielder Jose Hernandez; placed pitcher Bryan Bullington on the 60-day disabled list. |
| March 29, 2006 | Assigned pitchers Scott Strickland and Britt Reames and infielder Mike Edwards to minor league camp; optioned catcher Ronny Paulino and third baseman Jose Bautista to Indianapolis of the International League (AAA). |
| March 21, 2006 | Assigned pitchers Sean Burnett and Tom Gorzelanny, infielders Brad Eldred and Yurendell DeCaster and outfielder Rajai Davis to Indianapolis of the International League (AAA); assigned pitchers Ron Chiavacci, Nerio Rodriguez, Matt Whiteside, catcher Carlos Maldonado and infielders Jason Alfaro and Gookie Dawkins to minor league camp. |
| March 15, 2006 | Extended their player development contract with the Altoona Curve of the Eastern League (AA) through the 2010 season. |
| March 1, 2006 | Agreed to terms with shortstop Jack Wilson on a three-year contract extension. |
| February 16, 2006 | Extended their working agreement with Lynchburg of the Carolina League (A) through the 2008 season. |
| February 15, 2006 | Named Kent Tekulve major league advanced scout; released pitcher Joe Roa. |
| February 10, 2006 | Signed pitchers Matt Capps and Tom Gorzelanny, outfielder Rajai Davis and infielder Craig Stansberry to one-year contracts. |
| February 6, 2006 | Signed infielder Yurendall DeCaster to a one-year contract. |
| February 2, 2006 | Agreed to terms with pitcher Bryan Bullington. |
| January 19, 2006 | Signed pitcher Kip Wells to a one-year contract. |
| January 16, 2006 | Signed pitcher Oliver Perez to a one-year contract. |
| January 14, 2006 | Signed first baseman-outfielder Craig Wilson to a one-year contract. |
| January 6, 2006 | Signed pitchers Brandon Duckworth, Marty McLeary, C.J. Nitkowski, Nerio Rodriguez and Scott Strickland and infielder Gookie Dawkins to minor league contracts. |
| January 5, 2006 | Signed outfielder Jeromy Burnitz, who had been with the Chicago Cubs, to a one-year contract. |