| Round | Overall | Player |
|---|---|---|
| 1 | 5th | OF Ryan Braun Mil |
| 2 | 20th | 3B Kevin Youkilis Bos |
| 3 | 29th | 1B Joey Votto Cin |
| 4 | 44th | SP Jon Lester Bos |
| 5 | 53rd | SS Derek Jeter NYA |
| 6 | 68th | SP Tommy Hanson Atl |
| 7 | 77th | SP Ricky Nolasco Fla |
| 8 | 92nd | 3B Ian Stewart Col |
| 9 | 101st | RP Billy Wagner Atl |
| 10 | 116th | RP Ryan Franklin StL |
| 11 | 125th | DH Jorge Posada NYA |
| 12 | 140th | SP J.A. Happ Hou |
| 13 | 149th | SP Ryan Dempster ChN |
| 14 | 164th | 2B Jose Lopez Col |
| 15 | 173rd | OF Nolan Reimold Bal |
| 16 | 188th | SP David Price TB |
| 17 | 197th | OF Ryan Ludwick SD |
| 18 | 212th | OF Julio Borbon Tex |
| 19 | 221st | OF Chris Coghlan Fla |
| 20 | 236th | SP Shaun Marcum Mil |
| 21 | 245th | SP Hiroki Kuroda LAD |
| 22 | 260th | C Carlos Ruiz Phi |
| 23 | 269th | DH Jim Thome Min |
| 24 | 284th | SS Mike Aviles KC |
| 25 | 293rd | OF Juan Rivera LAA |
| 26 | 308th | SP Chris Volstad Fla |
| 27 | 317th | 3B Casey Mcgehee Mil |
| 28 | 332nd | OF Cameron Maybin SD |
| 29 | 341st | 1B Casey Kotchman Sea |