| Round | Overall | Player |
|---|---|---|
| 1 | 8th | SS Mike Young Tex |
| 2 | 17th | OF Jason Bay Pit |
| 3 | 32nd | SP Jake Peavy SD |
| 4 | 41st | 3B Eric Chavez Oak |
| 5 | 56th | RP Joe Nathan Min |
| 6 | 65th | OF Brian S. Giles SD |
| 7 | 80th | RP B.J. Ryan Tor |
| 8 | 89th | 2B Tadahito Iguchi ChA |
| 9 | 104th | OF Matt Holliday Col |
| 10 | 113th | 1B Justin Morneau Min |
| 11 | 128th | SP John Lackey LAA |
| 12 | 137th | OF Austin Kearns Was |
| 13 | 152nd | SP Doug Davis Ari |
| 14 | 161st | OF Josh Willingham Fla |
| 15 | 176th | SP Jon Lieber Phi |
| 16 | 185th | SP Aaron Harang Cin |
| 17 | 200th | 1B Dan Johnson Oak |
| 18 | 209th | SP Brad Radke Min |
| 19 | 224th | 2B Ron Belliard StL |
| 20 | 233rd | SP Paul Byrd Cle |
| 21 | 248th | SP Kelvim Escobar LAA |
| 22 | 257th | SP Jeff Weaver Sea |
| 23 | 272nd | 3B Corey Koskie Mil |
| 24 | 281st | SS Alex Gonzalez Bos |
| 25 | 296th | SP Ambiorix Burgos KC |
| 26 | 305th | OF Craig Monroe Det |
| 27 | 320th | OF Jeromy Burnitz Pit |
| 28 | 329th | RP Joey Devine Atl |
| 29 | 344th | C Danny Ardoin Bal |