| Round | Overall | Player |
|---|---|---|
| 1 | 8th | 1B Mark Teixeira NYA |
| 2 | 17th | SP Roy Halladay Phi |
| 3 | 32nd | OF Jason Bay NYN |
| 4 | 41st | 2B Aaron Hill Tor |
| 5 | 56th | SP Adam Wainwright StL |
| 6 | 65th | SP Cliff Lee Phi |
| 7 | 80th | OF Andre Ethier LAD |
| 8 | 89th | RP Heath Bell SD |
| 9 | 104th | RP Brian Fuentes Min |
| 10 | 113th | OF Michael Cuddyer Min |
| 11 | 128th | OF Torii Hunter LAA |
| 12 | 137th | SP Roy Oswalt Phi |
| 13 | 152nd | SS Yunel Escobar Tor |
| 14 | 161st | 3B Jorge Cantu Tex |
| 15 | 176th | C Kurt Suzuki Oak |
| 16 | 185th | SP Roberto Hernandez Cle |
| 17 | 200th | SP Brandon Webb Tex |
| 18 | 209th | SP Andy Pettitte NYA |
| 19 | 224th | 3B Kevin Kouzmanoff Oak |
| 20 | 233rd | SP Bronson Arroyo Cin |
| 21 | 248th | OF Marlon Byrd ChN |
| 22 | 257th | RP Fernando Rodney LAA |
| 23 | 272nd | C Rod Barajas NYN |
| 24 | 281st | OF Mike Cameron Bos |
| 25 | 296th | SP Justin Duchscherer Oak |
| 26 | 305th | SP Jason Marquis Was |
| 27 | 320th | 1B Jeff Clement Pit |
| 28 | 329th | 2B Luis Valbuena Cle |
| 29 | 344th | SS Tommy Manzella Hou |