| Round | Overall | Player |
|---|---|---|
| 1 | 12th | OF Melvin Upton TB |
| 2 | 13th | 2B Brandon Phillips Cin |
| 3 | 36th | SS Troy Tulowitzki Col |
| 4 | 37th | OF Hunter Pence Hou |
| 5 | 60th | 1B Adrian Gonzalez SD |
| 6 | 61st | 3B Chone Figgins LAA |
| 7 | 84th | 3B Mike Young Tex |
| 8 | 85th | C Jorge Posada NYA |
| 9 | 108th | SP John Maine NYN |
| 10 | 109th | SP Rich Harden ChN |
| 11 | 132nd | SP Philip Hughes NYA |
| 12 | 133rd | SP Dustin McGowan Tor |
| 13 | 156th | RP Rafael Soriano Atl |
| 14 | 157th | SP Dontrelle Willis Det |
| 15 | 180th | RP Todd Jones Det |
| 16 | 181st | OF Jack Cust Oak |
| 17 | 204th | OF Matt Kemp LAD |
| 18 | 205th | OF Jacoby Ellsbury Bos |
| 19 | 228th | OF Corey Patterson Cin |
| 20 | 229th | SP Mike Mussina NYA |
| 21 | 252nd | RP Jeremiah Accardo Tor |
| 22 | 253rd | SP Franklin Morales Col |
| 23 | 276th | SP Tim Wakefield Bos |
| 24 | 277th | OF Franklin Gutierrez Cle |
| 25 | 300th | OF Mike Cameron Mil |
| 26 | 301st | 1B Lyle Overbay Tor |
| 27 | 324th | 2B Brendan Harris Min |
| 28 | 325th | C Josh Bard Bos |
| 29 | 348th | 3B Greg Dobbs Phi |