| Free Agents | Pos. | Status |
| Joe Beimel | RP/LH | |
| Rafael Betancourt | RP/RH | Re-signed ($7.55 mil 2 yrs) |
| Alan Embree | RP/LH | |
| Jason Giambi | 1B | Re-signed (1 yr) |
| Juan Rincon | RP/RH | Re-signed (minor league deal) |
| Arbitration-Eligible | Pos. | Status |
| Clint Barmes | 2B | Re-signed ($3.225 mil, 1 yr) |
| Taylor Buchholz | RP/RH | Re-signed ($1.055 mil, 1 yr) |
| Jorge De La Rosa | SP/LH | Re-signed ($5.6 mil, 1 yr) |
| Jason Hammel | SP/RH | Re-signed ($1.9 mil, 1 yr) |
| Chris Iannetta | C | Re-signed ($8.3 mil, 3 yrs) |
| Ryan Spilborghs | LF | Re-signed ($3.6 mil, 2 yrs) |
| Huston Street | RP/RH | Re-signed ($22.5 mil, 3 yrs) |
| Acquired | Pos. | Status |
| Paul Lo Duca | C | Signed (minor league deal) |
| Alex Escobar | OF | Signed (minor league deal) |
| Chris Gissell | RP/RH | Signed (minor league deal) |
| Jimmy Gobble | SP/LH | Signed (minor league deal) |
| Robby Hammock | C | Signed (minor league deal) |
| Melvin Mora | 3B | Signed (from BAL, $1.3 mil, 1 yr) |
| Damian Moss | SP/LH | Signed (minor league deal) |
| Miguel Olivo | C | Signed (from KC, $2.5 mil, 1 yr) |
| Jay Payton | LF | Signed (minor league deal) |
| Josh Phelps | 1B | Signed (minor league deal) |
| Tim Redding | SP/RH | Signed (from NYM, minor league deal) |
| Bronson Sardinha | LF | Signed (minor league deal) |
| Departed | Pos. | Status |
| Garrett Atkins | 3B | Signed by BAL ($4 mil, 1 yr) |
| Jose Contreras | SP/RH | Signed with PHI ($1 mil, 1 yr) |
| Sal Fasano | C | Retired |
| Josh Fogg | SP/RH | Signed with NYM (minor league deal) |
| Matt Herges | RP/RH | Signed with KC (minor league deal) |
| Jason Marquis | SP/RH | Signed with WAS ($15 mil, 2 yrs) |
| Mike McCoy | 2B | Claimed off waivers by TOR |
| Matt Murton | LF | Signed in Japan |
| Joel Peralta | RP/RH | Signed with WAS (minor league deal) |
| Ryan Speier | RP/RH | Signed with WAS (minor league deal) |
| Yorvit Torrealba | C | Signed with SD ($1.25 mil, 1 yr) |
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