| Transactions | ||||||
| Date | Team | Player | Type | OthTm | EffDate | When |
| 4/24/2006 | EDG | Lester | Demoted to reserve roster |   |   | Before |
| 4/24/2006 | MUL | Correia | Promoted to active roster |   |   | Before |
| 6/4/2006 | CRH | League | Traded away | Pal |   | After |
| 6/4/2006 | CRH | Myers | Acquired via trade | Pal |   | After |
| 6/4/2006 | CRH | Renteria | Acquired via trade | Pal |   | After |
| 6/4/2006 | CRH | Schilling | Traded away | Pal |   | After |
| 6/12/2006 | WIZ | Marmol | Demoted to reserve roster |   |   | Before |
| 6/12/2006 | WIZ | Marte | Demoted to reserve roster |   |   | Before |
| 6/19/2006 | MID | Rowand | Demoted to reserve roster |   |   | Before |
| 6/25/2006 | COP | Lohse | Acquired via trade | MID |   | After |
| 6/25/2006 | COP | Wang | Traded away | MID |   | After |
| 6/25/2006 | MID | Lohse | Traded away | COP |   | After |
| 6/25/2006 | MID | Wang | Acquired via trade | COP |   | After |
| 6/26/2006 | COP | Lohse | Promoted to active roster |   |   | Before |
| 6/26/2006 | MID | Howell | Demoted to reserve roster |   |   | Before |
| 7/2/2006 | BT | Bonds | Traded away | WIZ |   | After |
| 7/2/2006 | BT | Hamels | Acquired via trade | WIZ |   | After |
| 7/2/2006 | WIZ | Bonds | Acquired via trade | BT |   | After |
| 7/2/2006 | WIZ | Hamels | Traded away | BT |   | After |
| 7/3/2006 | BT | Capuano | Demoted to reserve roster |   |   | Before |