| Round | Overall | Player |
|---|---|---|
| 1 | 11th | SP Roy Halladay Phi |
| 2 | 14th | SP Tim Lincecum SF |
| 3 | 35th | SP Ubaldo Jimenez Cle |
| 4 | 38th | DH Victor Martinez Det |
| 5 | 59th | RP Brian Wilson SF |
| 6 | 62nd | 1B Paul Konerko ChA |
| 7 | 83rd | 3B Pablo Sandoval SF |
| 8 | 86th | OF Alexis Rios ChA |
| 9 | 107th | OF Delmon Young Det |
| 10 | 110th | SS Elvis Andrus Tex |
| 11 | 131st | 2B Brian Roberts Bal |
| 12 | 134th | OF Curtis Granderson NYA |
| 13 | 155th | OF Jacoby Ellsbury Bos |
| 14 | 158th | SP Jonathan Sanchez KC |
| 15 | 179th | RP Kevin Gregg Bal |
| 16 | 182nd | SP Wandy Rodriguez Hou |
| 17 | 203rd | OF Luke Scott TB |
| 18 | 206th | RP J.J. Putz Ari |
| 19 | 227th | SS Yunel Escobar Tor |
| 20 | 230th | 3B Chone Figgins Sea |
| 21 | 251st | C Carlos Ruiz Phi |
| 22 | 254th | 3B Scott Rolen Cin |
| 23 | 275th | OF Domonic Brown Phi |
| 24 | 278th | SP Wade Davis TB |
| 25 | 299th | SP Joe Saunders Ari |
| 26 | 302nd | 2B Freddy Sanchez SF |
| 27 | 323rd | DH Jorge Posada NYA |
| 28 | 326th | 1B Lyle Overbay Ari |
| 29 | 347th | OF Desmond Jennings TB |