| Round | Overall | Player |
|---|---|---|
| 1 | 11th | 1B Lance Berkman Hou |
| 2 | 14th | 3B Miguel Cabrera Det |
| 3 | 35th | 3B Aramis Ramirez ChN |
| 4 | 38th | SS Jimmy Rollins Phi |
| 5 | 59th | SP Jered Weaver LAA |
| 6 | 62nd | 3B Bill Hall Mil |
| 7 | 83rd | SP Cole Hamels Phi |
| 8 | 86th | SP Daisuke Matsuzaka Bos |
| 9 | 107th | OF Michael Cuddyer Min |
| 10 | 110th | SP Adam Wainwright StL |
| 11 | 131st | 2B Josh Barfield Cle |
| 12 | 134th | SP Chien-Ming Wang NYA |
| 13 | 155th | OF Mark Teahen KC |
| 14 | 158th | 3B Alex Gordon KC |
| 15 | 179th | 3B Joe Crede ChA |
| 16 | 182nd | 3B Jorge Cantu Cin |
| 17 | 203rd | SP Jeremy Sowers Cle |
| 18 | 206th | OF Luke Scott Bal |
| 19 | 227th | 3B Ty Wigginton Hou |
| 20 | 230th | 1B Ryan Garko Cle |
| 21 | 251st | OF Craig Monroe Min |
| 22 | 254th | 1B Rich Aurilia SF |
| 23 | 275th | C Ronny Paulino Pit |
| 24 | 278th | SP Orlando Hernandez NYN |
| 25 | 299th | SP Pedro Martinez NYN |
| 26 | 302nd | SP Adam Loewen Bal |
| 27 | 323rd | RP Akinori Otsuka Tex |
| 28 | 326th | SP Russ Ortiz SF |
| 29 | 347th | C Yadier Molina StL |