| Round | Overall | Player |
|---|---|---|
| 1 | 2nd | 1B Ryan Howard Phi |
| 2 | 23rd | OF Jason Bay Pit |
| 3 | 26th | RP Francisco Rodriguez LAA |
| 4 | 47th | RP Joe Nathan Min |
| 5 | 50th | OF Hideki Matsui NYA |
| 6 | 71st | 3B Scott Rolen StL |
| 7 | 74th | SP Jason Schmidt LAD |
| 8 | 95th | SP Scott Kazmir TB |
| 9 | 98th | SP Erik Bedard Bal |
| 10 | 119th | 2B Howie Kendrick LAA |
| 11 | 122nd | OF J.D. Drew Bos |
| 12 | 143rd | SP Rich Hill ChN |
| 13 | 146th | RP Brian Fuentes Col |
| 14 | 167th | 1B Nomar Garciaparra LAD |
| 15 | 170th | C Jorge Posada NYA |
| 16 | 191st | 1B Adam LaRoche Pit |
| 17 | 194th | SP Roger Clemens NYA |
| 18 | 215th | SS Bobby Crosby Oak |
| 19 | 218th | SP Daniel Cabrera Bal |
| 20 | 239th | OF Shane Victorino Phi |
| 21 | 242nd | SS Troy Tulowitzki Col |
| 22 | 263rd | 3B Wilson Betemit NYA |
| 23 | 266th | OF Milton Bradley SD |
| 24 | 287th | SP Ricky Nolasco Fla |
| 25 | 290th | OF Chris Burke Ari |
| 26 | 311th | OF Marcus Thames Det |
| 27 | 314th | SP Doug Davis Ari |
| 28 | 335th | OF Melvin Upton TB |
| 29 | 338th | C John Buck KC |