| Round | Overall | Player |
|---|---|---|
| 1 | 7th | OF Ryan Braun Mil |
| 2 | 18th | OF Carlos Beltran NYN |
| 3 | 31st | 2B Brandon Phillips Cin |
| 4 | 42nd | SP Cole Hamels Phi |
| 5 | 55th | SP Daisuke Matsuzaka Bos |
| 6 | 66th | SP Roy Oswalt Hou |
| 7 | 79th | OF Magglio Ordonez Det |
| 8 | 90th | SP Edison Volquez Cin |
| 9 | 103rd | OF Vernon Wells Tor |
| 10 | 114th | 3B Mike Young Tex |
| 11 | 127th | 1B Adam LaRoche Ari |
| 12 | 138th | SS J.J. Hardy Min |
| 13 | 151st | SP Ted Lilly ChN |
| 14 | 162nd | RP B.J. Ryan Tor |
| 15 | 175th | SP Max Scherzer Det |
| 16 | 186th | C Kelly Shoppach Cle |
| 17 | 199th | SP John Maine NYN |
| 18 | 210th | OF Lastings Milledge Pit |
| 19 | 223rd | 1B Troy Glaus Atl |
| 20 | 234th | DH Hank Blalock Tex |
| 21 | 247th | SP Ubaldo Jimenez Col |
| 22 | 258th | 1B Todd Helton Col |
| 23 | 271st | RP Chris Perez StL |
| 24 | 282nd | 2B Clint Barmes Col |
| 25 | 295th | SP David Purcey Tor |
| 26 | 306th | 3B Casey Blake LAD |
| 27 | 319th | C Gerald Laird Det |
| 28 | 330th | SP Jeremy Bonderman Det |
| 29 | 343rd | RP Roy Corcoran Sea |