| Round | Overall | Player |
|---|---|---|
| 1 | 11th | 1B Miguel Cabrera Det |
| 2 | 14th | 1B Lance Berkman Hou |
| 3 | 35th | SP Brandon Webb Ari |
| 4 | 38th | 3B Chipper Jones Atl |
| 5 | 59th | C Russell Martin LAD |
| 6 | 62nd | SS Rafael Furcal LAD |
| 7 | 83rd | OF Carl Crawford TB |
| 8 | 86th | RP Brad Lidge Phi |
| 9 | 107th | SP Rich Harden Tex |
| 10 | 110th | SP Chien-Ming Wang NYA |
| 11 | 131st | RP Brian Fuentes LAA |
| 12 | 134th | RP Jonathan Broxton LAD |
| 13 | 155th | SP Mark Buehrle ChA |
| 14 | 158th | OF Milton Bradley Sea |
| 15 | 179th | 2B Howie Kendrick LAA |
| 16 | 182nd | OF Jayson Werth Phi |
| 17 | 203rd | SP Kenshin Kawakami Atl |
| 18 | 206th | OF Elijah Dukes Was |
| 19 | 227th | DH Jim Thome Min |
| 20 | 230th | SP Aaron Cook Col |
| 21 | 251st | SP Todd Wellemeyer StL |
| 22 | 254th | SS Orlando Cabrera Oak |
| 23 | 275th | C A.J. Pierzynski ChA |
| 24 | 278th | 3B Joe Crede Min |
| 25 | 299th | 1B Kendrys Morales LAA |
| 26 | 302nd | 2B Aaron Hill Tor |
| 27 | 323rd | OF Ryan Church Pit |
| 28 | 326th | SP Kevin Millwood Tex |
| 29 | 347th | 1B Lyle Overbay Tor |