| Round | Overall | Player |
|---|---|---|
| 1 | 10th | 1B Prince Fielder Mil |
| 2 | 15th | OF Magglio Ordonez Det |
| 3 | 34th | C Victor Martinez Cle |
| 4 | 39th | 3B Chipper Jones Atl |
| 5 | 58th | SP Roy Oswalt Hou |
| 6 | 63rd | SP Aaron Harang Cin |
| 7 | 82nd | SS Miguel Tejada Hou |
| 8 | 87th | DH Jim Thome ChA |
| 9 | 106th | RP Takashi Saito Bos |
| 10 | 111th | SP Francisco Liriano Min |
| 11 | 130th | RP Rafael Soriano Atl |
| 12 | 135th | SP Tim Hudson Atl |
| 13 | 154th | OF Jacoby Ellsbury Bos |
| 14 | 159th | SP Mark Buehrle ChA |
| 15 | 178th | OF Aaron Rowand SF |
| 16 | 183rd | 2B Kazuo Matsui Hou |
| 17 | 202nd | 1B Jason Giambi Oak |
| 18 | 207th | 2B Dustin Pedroia Bos |
| 19 | 226th | 3B Kevin Kouzmanoff SD |
| 20 | 231st | SP Aaron Cook Col |
| 21 | 250th | OF Jose Guillen KC |
| 22 | 255th | OF Mike Cameron Mil |
| 23 | 274th | OF Barry Bonds SF |
| 24 | 279th | SS Ryan Theriot ChN |
| 25 | 298th | SP Kevin Slowey Min |
| 26 | 303rd | C Johnny Estrada NYN |
| 27 | 322nd | RP Brian Wilson SF |
| 28 | 327th | SP Chad Gaudin ChN |
| 29 | 346th | SP Brandon McCarthy Tex |