| Round | Overall | Player |
|---|---|---|
| 1 | 1st | 1B Albert Pujols StL |
| 2 | 24th | SS Derek Jeter NYA |
| 3 | 25th | OF Andruw Jones Atl |
| 4 | 48th | RP Billy Wagner NYN |
| 5 | 49th | C Brian McCann Atl |
| 6 | 72nd | SP Justin Verlander Det |
| 7 | 73rd | SP Barry Zito SF |
| 8 | 96th | SP Dan Haren Ari |
| 9 | 97th | 3B Alex Gordon KC |
| 10 | 120th | OF Jeff Francoeur Atl |
| 11 | 121st | OF J.D. Drew Bos |
| 12 | 144th | 2B Brandon Phillips Cin |
| 13 | 145th | 3B Chone Figgins LAA |
| 14 | 168th | 2B Marcus Giles SD |
| 15 | 169th | RP Brad Lidge Phi |
| 16 | 192nd | OF Juan Pierre LAD |
| 17 | 193rd | SP Zach Duke Pit |
| 18 | 216th | RP Eric Gagne Hou |
| 19 | 217th | 1B Kevin Youkilis Bos |
| 20 | 240th | SP Boof Bonser Min |
| 21 | 241st | C Ronny Paulino Pit |
| 22 | 264th | 3B Wilson Betemit NYA |
| 23 | 265th | SP Ted Lilly ChN |
| 24 | 288th | 2B Freddy Sanchez Pit |
| 25 | 289th | SP Brandon McCarthy Tex |
| 26 | 312th | DH Mike Piazza Oak |
| 27 | 313th | SP Miguel Batista Sea |
| 28 | 336th | SP Doug Davis Ari |
| 29 | 337th | SS Omar Vizquel SF |