| Round | Overall | Player |
|---|---|---|
| 1 | 4th | C Joe Mauer Min |
| 2 | 21st | 3B Kevin Youkilis Bos |
| 3 | 28th | OF Jason Bay NYN |
| 4 | 45th | SP Tommy Hanson Atl |
| 5 | 52nd | 2B Dustin Pedroia Bos |
| 6 | 69th | 3B Chipper Jones Atl |
| 7 | 76th | SS Yunel Escobar Tor |
| 8 | 93rd | DH David Ortiz Bos |
| 9 | 100th | SP Tim Hudson Atl |
| 10 | 117th | RP Brian Fuentes Min |
| 11 | 124th | OF J.D. Drew Bos |
| 12 | 141st | DH Jim Thome Min |
| 13 | 148th | OF Johnny Damon Det |
| 14 | 165th | RP Billy Wagner Atl |
| 15 | 172nd | SS Rafael Furcal LAD |
| 16 | 189th | 3B Scott Rolen Cin |
| 17 | 196th | SP Derek Lowe Atl |
| 18 | 213th | C Ramon Hernandez Cin |
| 19 | 220th | 3B Mike Lowell Bos |
| 20 | 237th | SP J.A. Happ Hou |
| 21 | 244th | 1B Aubrey Huff SF |
| 22 | 261st | OF Jeff Francoeur Tex |
| 23 | 268th | 2B Kazuo Matsui Hou |
| 24 | 285th | SP Wade Davis TB |
| 25 | 292nd | SP Franklin Morales Col |
| 26 | 309th | RP Takashi Saito Atl |
| 27 | 316th | SP Ian Kennedy Ari |
| 28 | 333rd | OF Matt Diaz Pit |
| 29 | 340th | SS Edgar Renteria Cin |