| Round | Overall | Player |
|---|---|---|
| 1 | 12th | OF Matt Holliday Col |
| 2 | 13th | DH David Ortiz Bos |
| 3 | 36th | SP Brandon Webb Ari |
| 4 | 37th | SP Justin Verlander Det |
| 5 | 60th | SP Josh Beckett Bos |
| 6 | 61st | 3B Chipper Jones Atl |
| 7 | 84th | SP Scott Kazmir TB |
| 8 | 85th | OF Hunter Pence Hou |
| 9 | 108th | OF Andruw Jones LAD |
| 10 | 109th | 2B Kelly Johnson Atl |
| 11 | 132nd | SS Edgar Renteria Det |
| 12 | 133rd | C Geovany Soto ChN |
| 13 | 156th | SP Dustin McGowan Tor |
| 14 | 157th | 1B Kevin Youkilis Bos |
| 15 | 180th | SP Dontrelle Willis Det |
| 16 | 181st | OF Adam Jones Bal |
| 17 | 204th | OF Shane Victorino Phi |
| 18 | 205th | 2B Dustin Pedroia Bos |
| 19 | 228th | 3B Kevin Kouzmanoff SD |
| 20 | 229th | SP Tom Glavine Atl |
| 21 | 252nd | OF Carlos Quentin ChA |
| 22 | 253rd | OF Andre Ethier LAD |
| 23 | 276th | SP Mark Prior SD |
| 24 | 277th | SP Dave Bush Mil |
| 25 | 300th | SP Scott Baker Min |
| 26 | 301st | SS Alex Gonzalez Cin |
| 27 | 324th | OF Michael Bourn Hou |
| 28 | 325th | C Yadier Molina StL |
| 29 | 348th | OF Jordan Schafer Atl |