| Round | Overall | Player |
|---|---|---|
| 1 | 4th | 1B Joey Votto Cin |
| 2 | 21st | OF Carl Crawford Bos |
| 3 | 28th | 3B Kevin Youkilis Bos |
| 4 | 45th | SP David Price TB |
| 5 | 52nd | 2B Rickie Weeks Mil |
| 6 | 69th | C Carlos Santana Cle |
| 7 | 76th | SP C.J. Wilson LAA |
| 8 | 93rd | RP Carlos Marmol ChN |
| 9 | 100th | SP Carl Pavano Min |
| 10 | 117th | OF Nick Swisher NYA |
| 11 | 124th | DH David Ortiz Bos |
| 12 | 141st | OF Angel Pagan SF |
| 13 | 148th | RP Francisco Rodriguez Mil |
| 14 | 165th | OF Coco Crisp Oak |
| 15 | 172nd | SP Michael Pelfrey NYN |
| 16 | 189th | SP Derek Lowe Atl |
| 17 | 196th | SS Marcos Scutaro Bos |
| 18 | 213th | SP Jonathon Niese NYN |
| 19 | 220th | OF Corey Patterson STL |
| 20 | 237th | 1B Russ Branyan LAA |
| 21 | 244th | C Russell Martin NYA |
| 22 | 261st | OF Juan Pierre ChA |
| 23 | 268th | 1B Ty Wigginton Col |
| 24 | 285th | SP Brandon Webb Tex |
| 25 | 292nd | SP Vicente Padilla Bos |
| 26 | 309th | SP Chris Capuano NYN |
| 27 | 316th | 3B Kevin Kouzmanoff KC |
| 28 | 333rd | 2B Skip Schumaker StL |
| 29 | 340th | SS Alcides Escobar KC |