| Round | Overall | Player |
|---|---|---|
| 1 | 1st | 1B Albert Pujols StL |
| 2 | 24th | 3B Mark Reynolds Bal |
| 3 | 25th | DH Victor Martinez Det |
| 4 | 48th | 2B Ben Zobrist TB |
| 5 | 49th | SS Derek Jeter NYA |
| 6 | 72nd | OF Carlos Quentin ChA |
| 7 | 73rd | SP Chad Billingsley LAD |
| 8 | 96th | SP Jered Weaver LAA |
| 9 | 97th | SP Ricky Nolasco Fla |
| 10 | 120th | OF Nick Swisher NYA |
| 11 | 121st | SP Carlos Zambrano ChN |
| 12 | 144th | 1B Brad Hawpe SD |
| 13 | 145th | OF Michael Cuddyer Min |
| 14 | 168th | SP J.A. Happ Hou |
| 15 | 169th | 1B James Loney LAD |
| 16 | 192nd | SP Joe Saunders Ari |
| 17 | 193rd | RP Brad Lidge Phi |
| 18 | 216th | SP Aaron Harang SD |
| 19 | 217th | OF Mike Cameron Bos |
| 20 | 240th | C Mike Napoli LAA |
| 21 | 241st | 2B Clint Barmes Col |
| 22 | 264th | SS Jhonny Peralta Det |
| 23 | 265th | RP Octavio Dotel Tor |
| 24 | 288th | OF Corey Hart Mil |
| 25 | 289th | SP Kevin Millwood Bal |
| 26 | 312th | RP Kerry Wood NYA |