| Round | Overall | Player |
|---|---|---|
| 1 | 5th | 2B Chase Utley Phi |
| 2 | 20th | 1B Justin Morneau Min |
| 3 | 29th | SP Johan Santana NYN |
| 4 | 44th | C Brian McCann Atl |
| 5 | 53rd | OF Andre Ethier LAD |
| 6 | 68th | RP Brian Fuentes Min |
| 7 | 77th | RP Heath Bell SD |
| 8 | 92nd | SP John Lackey Bos |
| 9 | 101st | OF Andrew McCutchen Pit |
| 10 | 116th | 3B Chipper Jones Atl |
| 11 | 125th | 1B Brad Hawpe SD |
| 12 | 140th | SP J.A. Happ Hou |
| 13 | 149th | 3B Jorge Cantu Tex |
| 14 | 164th | SS Rafael Furcal LAD |
| 15 | 173rd | DH David Ortiz Bos |
| 16 | 188th | SP Kevin Slowey Min |
| 17 | 197th | SP Aaron Harang SD |
| 18 | 212th | SS Jhonny Peralta Det |
| 19 | 221st | 1B Troy Glaus Atl |
| 20 | 236th | SP Nick Blackburn Min |
| 21 | 245th | C Jarrod Saltalamacchia Bos |
| 22 | 260th | OF Nyjer Morgan Was |
| 23 | 269th | 2B Adam Kennedy Sea |
| 24 | 284th | OF Austin Jackson Det |
| 25 | 293rd | 3B Pedro Alvarez Pit |
| 26 | 308th | RP Octavio Dotel Tor |
| 27 | 317th | SS Cristian Guzman Tex |
| 28 | 332nd | SP Tom Gorzelanny ChN |
| 29 | 341st | SP Jon Garland LAD |