| Round | Overall | Player |
|---|---|---|
| 1 | 11th | SP Johan Santana Min |
| 2 | 14th | OF Adam Dunn Cin |
| 3 | 35th | 3B Hank Blalock Tex |
| 4 | 38th | 2B Rickie Weeks Mil |
| 5 | 59th | SS Jimmy Rollins Phi |
| 6 | 62nd | SP Randy Johnson NYA |
| 7 | 83rd | OF Jim Edmonds StL |
| 8 | 86th | 1B Prince Fielder Mil |
| 9 | 107th | OF Jonny Gomes TB |
| 10 | 110th | SP Livan Hernandez Ari |
| 11 | 131st | 1B Justin Morneau Min |
| 12 | 134th | SP Scott Kazmir TB |
| 13 | 155th | OF Josh Willingham Fla |
| 14 | 158th | OF Austin Kearns Was |
| 15 | 179th | SP Brad Penny LAD |
| 16 | 182nd | RP Chris Ray Bal |
| 17 | 203rd | 3B Edwin Encarnacion Cin |
| 18 | 206th | SP Ervin Santana LAA |
| 19 | 227th | SP Jeff Suppan Mil |
| 20 | 230th | OF Rocco Baldelli TB |
| 21 | 251st | RP Mike Gonzalez Atl |
| 22 | 254th | RP Chris Reitsma Atl |
| 23 | 275th | OF Milton Bradley Oak |
| 24 | 278th | 2B Luis A. Gonzalez Col |
| 25 | 299th | SP Jason Vargas Fla |
| 26 | 302nd | C Danny Ardoin Bal |
| 27 | 323rd | OF Nick Markakis Bal |
| 28 | 326th | SP Dave Bush Mil |
| 29 | 347th | SS David Eckstein StL |