| Round | Overall | Player |
|---|---|---|
| 1 | 8th | SS Jose Reyes NYN |
| 2 | 17th | OF Ryan Braun Mil |
| 3 | 32nd | OF Ichiro Suzuki Sea |
| 4 | 41st | OF Magglio Ordonez Det |
| 5 | 56th | 2B Brian Roberts Bal |
| 6 | 65th | SP Aaron Harang Cin |
| 7 | 80th | 3B Adrian Beltre Sea |
| 8 | 89th | SP Roberto Hernandez Cle |
| 9 | 104th | RP Takashi Saito Bos |
| 10 | 113th | SP A.J. Burnett Tor |
| 11 | 128th | SP Kelvim Escobar LAA |
| 12 | 137th | RP Brad Lidge Phi |
| 13 | 152nd | C Ben Molina SF |
| 14 | 161st | SP Joba Chamberlain NYA |
| 15 | 176th | 1B Kevin Youkilis Bos |
| 16 | 185th | SP Ian Snell Pit |
| 17 | 200th | OF Michael Cuddyer Min |
| 18 | 209th | SP Andy Pettitte NYA |
| 19 | 224th | OF Johnny Damon NYA |
| 20 | 233rd | 2B Orlando Hudson Ari |
| 21 | 248th | 3B Juan Uribe SF |
| 22 | 257th | OF Melky Cabrera NYA |
| 23 | 272nd | SP C.J. Wilson Tex |
| 24 | 281st | 1B Dmitri Young Was |
| 25 | 296th | SP Orlando Hernandez NYN |
| 26 | 305th | RP Jeremiah Accardo Tor |
| 27 | 320th | 3B Brandon Inge Det |
| 28 | 329th | OF Jose Guillen KC |
| 29 | 344th | C Gregg Zaun Bal |