| Round | Overall | Player |
|---|---|---|
| 1 | 4th | 3B Alex Rodriguez NYA |
| 2 | 21st | 2B Ian Kinsler Tex |
| 3 | 28th | 1B Joey Votto Cin |
| 4 | 45th | OF Jason Bay NYN |
| 5 | 52nd | 1B Adam Lind Tor |
| 6 | 69th | SP Josh Beckett Bos |
| 7 | 76th | SP Javier Vazquez Fla |
| 8 | 93rd | OF Lance Berkman STL |
| 9 | 100th | RP Francisco Rodriguez NYN |
| 10 | 117th | SP A.J. Burnett NYA |
| 11 | 124th | SP Carlos Zambrano ChN |
| 12 | 141st | SS Yunel Escobar Tor |
| 13 | 148th | DH Jason Kubel Min |
| 14 | 165th | SP Scott Kazmir LAA |
| 15 | 172nd | RP Trevor Hoffman Ret |
| 16 | 189th | C Miguel Montero Ari |
| 17 | 196th | OF Vernon Wells Tor |
| 18 | 213th | SP Aaron Harang SD |
| 19 | 220th | RP Kerry Wood NYA |
| 20 | 237th | SP Daisuke Matsuzaka Bos |
| 21 | 244th | 2B Kelly Johnson Ari |
| 22 | 261st | SS Erick Aybar LAA |
| 23 | 268th | SP Chris Volstad Fla |
| 24 | 285th | 3B Brandon Wood LAA |
| 25 | 292nd | OF Juan Rivera LAA |
| 26 | 309th | OF Cameron Maybin SD |
| 27 | 316th | 1B Lyle Overbay Tor |
| 28 | 333rd | SP John Maine NYN |
| 29 | 340th | C Jarrod Saltalamacchia Bos |