| Round | Overall | Player |
|---|---|---|
| 1 | 10th | SP Johan Santana Min |
| 2 | 15th | DH Jim Thome ChA |
| 3 | 34th | 3B Eric Chavez Oak |
| 4 | 39th | RP Brad Lidge Hou |
| 5 | 58th | OF Andruw Jones Atl |
| 6 | 63rd | RP Joe Nathan Min |
| 7 | 82nd | SS Rafael Furcal Atl |
| 8 | 87th | SP Roger Clemens Hou |
| 9 | 106th | SP A.J. Burnett Fla |
| 10 | 111th | C Jason Varitek Bos |
| 11 | 130th | OF Brad Wilkerson Was |
| 12 | 135th | SP Odalis Perez LAD |
| 13 | 154th | 2B Aaron Miles Col |
| 14 | 159th | SP Jeremy Bonderman Det |
| 15 | 178th | OF Steve Finley LAA |
| 16 | 183rd | SP Bobby Madritsch Sea |
| 17 | 202nd | SP Joel Pineiro Sea |
| 18 | 207th | SS Jack Wilson Pit |
| 19 | 226th | 3B Garrett Atkins Col |
| 20 | 231st | 1B Adam LaRoche Atl |
| 21 | 250th | SP Luke Hudson Cin |
| 22 | 255th | OF Milton Bradley LAD |
| 23 | 274th | SP Dan Haren Oak |
| 24 | 279th | C A.J. Pierzynski ChA |
| 25 | 298th | 2B Chris Burke Hou |
| 26 | 303rd | OF Craig A. Wilson Pit |
| 27 | 322nd | OF Jeremy Reed Sea |
| 28 | 327th | SP Felix Hernandez Sea |
| 29 | 346th | SP Tony Armas Jr. Was |