| Sunday, January 1st, 2006 |
| Fired general manager R. Sousa. |
| Drafted CF A. Dufresne in the 2006 inaugural draft (Round 1, Pick 2, 2nd overall Pick). |
| Drafted RF S. Audley in the 2006 inaugural draft (Round 2, Pick 2, 4th overall Pick). |
| Drafted C J. Rodríguez in the 2006 inaugural draft (Round 3, Pick 2, 6th overall Pick). |
| Drafted SP G. León in the 2006 inaugural draft (Round 4, Pick 2, 8th overall Pick). |
| Drafted LF A. Nickles in the 2006 inaugural draft (Round 5, Pick 2, 10th overall Pick). |
| Drafted SP A. Bautista in the 2006 inaugural draft (Round 6, Pick 2, 12th overall Pick). |
| Drafted SP W. O'Neal in the 2006 inaugural draft (Round 7, Pick 2, 14th overall Pick). |
| Drafted CL B. Méndez in the 2006 inaugural draft (Round 8, Pick 2, 16th overall Pick). |
| Drafted C F. Salas in the 2006 inaugural draft (Round 9, Pick 2, 18th overall Pick). |
| Drafted 1B P. Hoskins in the 2006 inaugural draft (Round 10, Pick 2, 20th overall Pick). |
| Drafted SS R. Requena in the 2006 inaugural draft (Round 11, Pick 2, 22nd overall Pick). |
| Drafted SP J. Bavin in the 2006 inaugural draft (Round 12, Pick 2, 24th overall Pick). |
| Drafted MR M. Prando in the 2006 inaugural draft (Round 13, Pick 2, 26th overall Pick). |
| Drafted SP R. Esquivel in the 2006 inaugural draft (Round 14, Pick 2, 28th overall Pick). |
| Drafted 3B B. Ayliffe in the 2006 inaugural draft (Round 15, Pick 2, 30th overall Pick). |
| Drafted 2B Y. Williams in the 2006 inaugural draft (Round 16, Pick 2, 32nd overall Pick). |
| Drafted MR D. Haynes in the 2006 inaugural draft (Round 17, Pick 2, 34th overall Pick). |
| Drafted MR C. Gallahur in the 2006 inaugural draft (Round 18, Pick 2, 36th overall Pick). |
| Drafted MR D. Rabelas in the 2006 inaugural draft (Round 19, Pick 2, 38th overall Pick). |
| Drafted MR P. Pouden in the 2006 inaugural draft (Round 20, Pick 2, 40th overall Pick). |
| Drafted RF B. Coslett in the 2006 inaugural draft (Round 21, Pick 2, 42nd overall Pick). |
| Drafted C K. Buytelaar in the 2006 inaugural draft (Round 22, Pick 2, 44th overall Pick). |
| Drafted CF R. Servera in the 2006 inaugural draft (Round 23, Pick 2, 46th overall Pick). |
| Drafted 3B A. Vázquez in the 2006 inaugural draft (Round 24, Pick 2, 48th overall Pick). |
| Drafted SP S. Hanson in the 2006 inaugural draft (Round 25, Pick 2, 50th overall Pick). |
| Drafted CF L. Santos in the 2006 inaugural draft (Round 26, Pick 2, 52nd overall Pick). |
| Drafted SP B. Durberville in the 2006 inaugural draft (Round 27, Pick 2, 54th overall Pick). |
| Drafted LF D. Newdigate in the 2006 inaugural draft (Round 28, Pick 2, 56th overall Pick). |
| Drafted C M. Kiser in the 2006 inaugural draft (Round 29, Pick 2, 58th overall Pick). |
| Drafted SP M. O'Quinlan in the 2006 inaugural draft (Round 30, Pick 2, 60th overall Pick). |
| Drafted CL T. Day in the 2006 inaugural draft (Round 31, Pick 2, 62nd overall Pick). |
| Drafted RF M. Morales in the 2006 inaugural draft (Round 32, Pick 2, 64th overall Pick). |
| Drafted 3B E. Vanlandingham in the 2006 inaugural draft (Round 33, Pick 2, 66th overall Pick). |
| Drafted SP J. O'Breslin in the 2006 inaugural draft (Round 34, Pick 2, 68th overall Pick). |
| Drafted SS M. Geis in the 2006 inaugural draft (Round 35, Pick 2, 70th overall Pick). |
| Drafted C R. Visaya in the 2006 inaugural draft (Round 36, Pick 2, 72nd overall Pick). |
| Drafted MR T. Lyons in the 2006 inaugural draft (Round 37, Pick 2, 74th overall Pick). |
| Drafted MR T. Hairston in the 2006 inaugural draft (Round 38, Pick 2, 76th overall Pick). |
| Drafted 2B B. Bradford in the 2006 inaugural draft (Round 39, Pick 2, 78th overall Pick). |
| Drafted SP C. Bieber in the 2006 inaugural draft (Round 40, Pick 2, 80th overall Pick). |
| Drafted 2B D. DeBoer in the 2006 inaugural draft (Round 41, Pick 2, 82nd overall Pick). |
| Drafted RF C. Price in the 2006 inaugural draft (Round 42, Pick 2, 84th overall Pick). |
| Drafted RF F. Shumaker in the 2006 inaugural draft (Round 43, Pick 2, 86th overall Pick). |
| Released SP A. Bautista. |
| Released SP J. Bavin. |
| Released SP R. Esquivel. |
| Released SP G. León. |
| Released SP W. O'Neal. |
| Released MR C. Gallahur. |
| Released MR D. Haynes. |
| Released MR M. Prando. |
| Released MR D. Rabelas. |
| Released CL B. Méndez. |
| Released C F. Salas. |
| Released C K. Buytelaar. |
| Released C J. Rodríguez. |
| Released 1B P. Hoskins. |
| Released 2B Y. Williams. |
| Released 3B B. Ayliffe. |
| Released 3B A. Vázquez. |
| Released SS R. Requena. |
| Released CF A. Dufresne. |
| Released LF A. Nickles. |
| Released RF S. Audley. |
| Released RF B. Coslett. |
| Released RF M. Morales. |
| Placed SP C. Bieber on the active roster. |
| Placed SP B. Durberville on the active roster. |
| Placed SP S. Hanson on the active roster. |
| Placed SP J. O'Breslin on the active roster. |
| Placed SP M. O'Quinlan on the active roster. |
| Placed MR T. Lyons on the active roster. |
| Placed MR T. Hairston on the active roster. |
| Placed MR P. Pouden on the active roster. |
| Placed CL T. Day on the active roster. |
| Placed C R. Visaya on the active roster. |
| Placed C M. Kiser on the active roster. |
| Placed 2B B. Bradford on the active roster. |
| Placed 2B D. DeBoer on the active roster. |
| Placed 3B E. Vanlandingham on the active roster. |
| Placed SS M. Geis on the active roster. |
| Placed LF D. Newdigate on the active roster. |
| Placed CF L. Santos on the active roster. |
| Placed CF R. Servera on the active roster. |
| Placed RF C. Price on the active roster. |
| Placed RF F. Shumaker on the active roster. |
| Released SP C. Bieber. |
| Released SP B. Durberville. |
| Released SP S. Hanson. |
| Released SP J. O'Breslin. |
| Released SP M. O'Quinlan. |
| Released MR T. Hairston. |
| Released MR P. Pouden. |
| Released MR T. Lyons. |
| Released CL T. Day. |
| Released C M. Kiser. |
| Released C R. Visaya. |
| Released 2B B. Bradford. |
| Released 2B D. DeBoer. |
| Released 3B E. Vanlandingham. |
| Released SS M. Geis. |
| Released LF D. Newdigate. |
| Released CF L. Santos. |
| Released CF R. Servera. |
| Released RF C. Price. |
| Released RF F. Shumaker. |
| Placed SP J. Bonderman on the active roster. |
| Placed SP C. Capuano on the active roster. |
| Placed SP R. Halladay on the active roster. |
| Placed SP P. Martinez on the active roster. |
| Placed SP M. Mussina on the active roster. |
| Placed CL T. Gordon on the active roster. |
| Placed CL T. Hoffman on the active roster. |
| Placed CL B. Ryan on the active roster. |
| Placed CL B. Wagner on the active roster. |
| Placed C V. Martinez on the active roster. |
| Placed C J. Estrada on the active roster. |
| Placed 1B J. Thome on the active roster. |
| Placed 1B A. Pujols on the active roster. |
| Placed 2B C. Utley on the active roster. |
| Placed 3B D. Wright on the active roster. |
| Placed SS J. Reyes on the active roster. |
| Placed SS M. Tejada on the active roster. |
| Placed SS N. Garciaparra on the active roster. |
| Placed LF M. Cabrera on the active roster. |
| Placed LF M. Ramirez on the active roster. |
| Placed LF C. Crawford on the active roster. |
| Placed CF C. Beltran on the active roster. |
| Placed CF V. Wells on the active roster. |
