| Round | Overall | Player |
|---|---|---|
| 1 | 11th | 1B Mark Teixeira NYA |
| 2 | 14th | OF Josh Hamilton Tex |
| 3 | 35th | OF Carlos Lee Hou |
| 4 | 38th | SP Cole Hamels Phi |
| 5 | 59th | SP Jon Lester Bos |
| 6 | 62nd | OF Ryan Ludwick StL |
| 7 | 83rd | SP A.J. Burnett NYA |
| 8 | 86th | RP Mariano Rivera NYA |
| 9 | 107th | 3B Garrett Atkins Bal |
| 10 | 110th | SP Justin Verlander Det |
| 11 | 131st | OF Corey Hart Mil |
| 12 | 134th | SP Joba Chamberlain NYA |
| 13 | 155th | SP Chris Carpenter StL |
| 14 | 158th | 2B Rickie Weeks Mil |
| 15 | 179th | RP Troy Percival TB |
| 16 | 182nd | OF Jayson Werth Phi |
| 17 | 203rd | C Ivan Rodriguez Hou |
| 18 | 206th | SS Khalil Greene Tex |
| 19 | 227th | C Jarrod Saltalamacchia Tex |
| 20 | 230th | SP Edwin Jackson Ari |
| 21 | 251st | DH Travis Hafner Cle |
| 22 | 254th | 1B Kendrys Morales LAA |
| 23 | 275th | 3B Josh Fields KC |
| 24 | 278th | RP Jason Motte StL |
| 25 | 299th | SS Erick Aybar LAA |
| 26 | 302nd | SP Jamie Moyer Phi |
| 27 | 323rd | 2B Chris Getz KC |
| 28 | 326th | OF Ryan Spilborghs Col |
| 29 | 347th | SP Daniel Cabrera Bal |