| Round | Overall | Player |
|---|---|---|
| 1 | 5th | C Joe Mauer Min |
| 2 | 20th | OF Matt Holliday StL |
| 3 | 29th | SS Jimmy Rollins Phi |
| 4 | 44th | OF Jason Bay NYN |
| 5 | 53rd | SP Chris Carpenter StL |
| 6 | 68th | OF Shin-Soo Choo Cle |
| 7 | 77th | 1B Kendrys Morales LAA |
| 8 | 92nd | RP Brian Fuentes Min |
| 9 | 101st | RP Brian Wilson SF |
| 10 | 116th | SP Wandy Rodriguez Hou |
| 11 | 125th | 3B Ian Stewart Col |
| 12 | 140th | RP Ryan Franklin StL |
| 13 | 149th | OF Nate McLouth Atl |
| 14 | 164th | SP Derek Lowe Atl |
| 15 | 173rd | 2B Jose Lopez Col |
| 16 | 188th | SP Hiroki Kuroda LAD |
| 17 | 197th | C Russell Martin NYA |
| 18 | 212th | SP Jeff Niemann TB |
| 19 | 221st | SP John Maine NYN |
| 20 | 236th | SP Brandon Morrow Tor |
| 21 | 245th | SP Anibal Sanchez Fla |
| 22 | 260th | 1B Russ Branyan Sea |
| 23 | 269th | 3B Casey Blake LAD |
| 24 | 284th | OF Juan Pierre ChA |
| 25 | 293rd | SS Ryan Theriot STL |
| 26 | 308th | 3B Placido Polanco Phi |