| Round | Overall | Player |
|---|---|---|
| 1 | 1st | 1B Albert Pujols StL |
| 2 | 24th | 3B Garrett Atkins Col |
| 3 | 25th | OF Matt Holliday Col |
| 4 | 48th | C Victor Martinez Cle |
| 5 | 49th | SP Roy Oswalt Hou |
| 6 | 72nd | RP Huston Street Oak |
| 7 | 73rd | SP C.C. Sabathia Cle |
| 8 | 96th | SP Ben Sheets Mil |
| 9 | 97th | 2B Dan Uggla Fla |
| 10 | 120th | 1B Prince Fielder Mil |
| 11 | 121st | SP Aaron Harang Cin |
| 12 | 144th | OF Raul Ibanez Sea |
| 13 | 145th | SP Dave Bush Mil |
| 14 | 168th | 3B Eric Chavez Oak |
| 15 | 169th | RP Chad Cordero Was |
| 16 | 192nd | SS Stephen Drew Ari |
| 17 | 193rd | SP Rich Hill ChN |
| 18 | 216th | OF Luke Scott Bal |
| 19 | 217th | SP Kei Igawa NYA |
| 20 | 240th | OF Chris Young Ari |
| 21 | 241st | SP Carl Pavano NYA |
| 22 | 264th | 2B Marcus Giles SD |
| 23 | 265th | SS Troy Tulowitzki Col |
| 24 | 288th | OF Chris Burke Ari |
| 25 | 289th | SP Brandon McCarthy Tex |
| 26 | 312th | C Josh Bard SD |
| 27 | 313th | 1B James Loney LAD |
| 28 | 336th | 3B Andy LaRoche LAD |
| 29 | 337th | SP Russ Ortiz SF |