| Round | Overall | Player |
|---|---|---|
| 1 | 11th | SS Jimmy Rollins Phi |
| 2 | 14th | DH David Ortiz Bos |
| 3 | 35th | OF Curtis Granderson Det |
| 4 | 38th | C Russell Martin LAD |
| 5 | 59th | 3B Chipper Jones Atl |
| 6 | 62nd | OF Hunter Pence Hou |
| 7 | 83rd | 2B Rickie Weeks Mil |
| 8 | 86th | OF Josh Hamilton Tex |
| 9 | 107th | SP John Smoltz Bos |
| 10 | 110th | RP Bobby Jenks ChA |
| 11 | 131st | SP Brett Myers Phi |
| 12 | 134th | SP Chad Billingsley LAD |
| 13 | 155th | SP Ben Sheets Mil |
| 14 | 158th | SP Oliver Perez NYN |
| 15 | 179th | 1B Todd Helton Col |
| 16 | 182nd | SP Bronson Arroyo Cin |
| 17 | 203rd | RP Kerry Wood ChN |
| 18 | 206th | RP Troy Percival TB |
| 19 | 227th | 1B Nick Johnson Was |
| 20 | 230th | OF Jack Cust Oak |
| 21 | 251st | SP Randy Johnson Ari |
| 22 | 254th | SP Ubaldo Jimenez Col |
| 23 | 275th | OF Milton Bradley ChN |
| 24 | 278th | RP Brandon Lyon Det |
| 25 | 299th | 3B Melvin Mora Bal |
| 26 | 302nd | RP Tony Pena Ari |
| 27 | 323rd | 2B Luis Castillo NYN |
| 28 | 326th | SS Jack Wilson Pit |
| 29 | 347th | C Yadier Molina StL |