| Round | Overall | Player |
|---|---|---|
| 1 | 2nd | C Joe Mauer Min |
| 2 | 23rd | SP Roy Halladay Phi |
| 3 | 26th | OF Grady Sizemore Cle |
| 4 | 47th | OF Nelson Cruz Tex |
| 5 | 50th | SP Adam Wainwright StL |
| 6 | 71st | SP Cole Hamels Phi |
| 7 | 74th | OF Adam Jones Bal |
| 8 | 95th | 2B Gordon Beckham ChA |
| 9 | 98th | DH Mike Young Tex |
| 10 | 119th | OF Jason Heyward ATL |
| 11 | 122nd | SS Jason Bartlett SD |
| 12 | 143rd | SP Tim Hudson Atl |
| 13 | 146th | 1B Chris Davis Tex |
| 14 | 167th | SP Rich Harden Oak |
| 15 | 170th | RP Ryan Franklin StL |
| 16 | 191st | 1B Paul Konerko ChA |
| 17 | 194th | 3B Chone Figgins Sea |
| 18 | 215th | 1B Matt LaPorta Cle |
| 19 | 218th | RP Mike Gonzalez Bal |
| 20 | 239th | OF Kyle Blanks SD |
| 21 | 242nd | 3B Eric Chavez Oak |
| 22 | 263rd | SP Joe Blanton Phi |
| 23 | 266th | SS Mike Aviles KC |
| 24 | 287th | C Kelly Shoppach TB |
| 25 | 290th | 2B Akinori Iwamura Pit |
| 26 | 311th | SP Chris Young SD |
| 27 | 314th | RP Octavio Dotel Tor |
| 28 | 335th | SP Ryan Madson Phi |
| 29 | 338th | RP J.J. Putz Ari |