| Round | Overall | Player |
|---|---|---|
| 1 | 5th | OF Matt Holliday Col |
| 2 | 20th | OF Vladimir Guerrero LAA |
| 3 | 29th | SP Jake Peavy SD |
| 4 | 44th | DH Travis Hafner Cle |
| 5 | 53rd | RP Francisco Rodriguez LAA |
| 6 | 68th | 2B Dan Uggla Fla |
| 7 | 77th | SP Carlos Zambrano ChN |
| 8 | 92nd | 1B Todd Helton Col |
| 9 | 101st | SP Brad Penny LAD |
| 10 | 116th | DH Hank Blalock Tex |
| 11 | 125th | OF Delmon Young Min |
| 12 | 140th | SP Matt Cain SF |
| 13 | 149th | RP Jose Valverde Hou |
| 14 | 164th | 1B Billy Butler KC |
| 15 | 173rd | C Geovany Soto ChN |
| 16 | 188th | SS Bobby Crosby Oak |
| 17 | 197th | SS Stephen Drew Ari |
| 18 | 212th | OF Michael Cuddyer Min |
| 19 | 221st | SP Carlos Silva Sea |
| 20 | 236th | SP Bartolo Colon ChA |
| 21 | 245th | OF Justin Upton Ari |
| 22 | 260th | 2B Mark Ellis Oak |
| 23 | 269th | SP Paul Maholm Pit |
| 24 | 284th | C Kurt Suzuki Oak |
| 25 | 293rd | SP Andrew Miller Fla |
| 26 | 308th | OF Jason Kubel Min |
| 27 | 317th | 3B Jorge Cantu Fla |
| 28 | 332nd | OF Andre Ethier LAD |
| 29 | 341st | SP Kyle Kendrick Phi |