| Round | Overall | Player |
|---|---|---|
| 1 | 11th | 1B Miguel Cabrera Det |
| 2 | 14th | 3B David Wright NYN |
| 3 | 35th | OF Jayson Werth Was |
| 4 | 38th | 2B Robinson Cano NYA |
| 5 | 59th | OF Nick Markakis Bal |
| 6 | 62nd | SP Josh Beckett Bos |
| 7 | 83rd | SP Yovani Gallardo Mil |
| 8 | 86th | OF Melvin Upton TB |
| 9 | 107th | OF Carlos Lee Hou |
| 10 | 110th | SP Javier Vazquez Fla |
| 11 | 131st | RP Bobby Jenks Bos |
| 12 | 134th | SS Alexei Ramirez ChA |
| 13 | 155th | DH David Ortiz Bos |
| 14 | 158th | SP Tim Hudson Atl |
| 15 | 179th | C Russell Martin NYA |
| 16 | 182nd | SP Jonathan Sanchez SF |
| 17 | 203rd | SP Rich Harden Oak |
| 18 | 206th | SP Aaron Harang SD |
| 19 | 227th | SS Elvis Andrus Tex |
| 20 | 230th | RP Huston Street Col |
| 21 | 251st | SP Scott Feldman Tex |
| 22 | 254th | OF Corey Hart Mil |
| 23 | 275th | 2B Scott Sizemore Det |
| 24 | 278th | 1B Gaby Sanchez Fla |
| 25 | 299th | OF Delmon Young Min |
| 26 | 302nd | 3B Chase Headley SD |
| 27 | 323rd | SP Aaron Cook Col |
| 28 | 326th | C John Buck Fla |
| 29 | 347th | RP Octavio Dotel Tor |