| Round | Overall | Player |
|---|---|---|
| 1 | 6th | 1B Miguel Cabrera Det |
| 2 | 19th | SP Jake Peavy SD |
| 3 | 30th | SP Brandon Webb Ari |
| 4 | 43rd | SS Derek Jeter NYA |
| 5 | 54th | 1B Paul Konerko ChA |
| 6 | 67th | RP J.J. Putz Sea |
| 7 | 78th | 2B Dan Uggla Fla |
| 8 | 91st | OF Nick Swisher ChA |
| 9 | 102nd | OF Delmon Young Min |
| 10 | 115th | OF Jeremy Hermida Fla |
| 11 | 126th | SP John Maine NYN |
| 12 | 139th | OF Rick Ankiel StL |
| 13 | 150th | 1B Ryan Garko Cle |
| 14 | 163rd | OF Raul Ibanez Sea |
| 15 | 174th | SS Orlando Cabrera ChA |
| 16 | 187th | C Jason Varitek Bos |
| 17 | 198th | RP Carlos Marmol ChN |
| 18 | 211th | SP Jake Westbrook Cle |
| 19 | 222nd | SP Nate Robertson Det |
| 20 | 235th | 3B Casey Blake LAD |
| 21 | 246th | 2B Freddy Sanchez Pit |
| 22 | 259th | SP Homer Bailey Cin |
| 23 | 270th | RP Brian Wilson SF |
| 24 | 283rd | SP Aaron Cook Col |
| 25 | 294th | C Yorvit Torrealba Col |
| 26 | 307th | SP Kyle Kendrick Phi |
| 27 | 318th | 1B Shelley Duncan NYA |
| 28 | 331st | OF Xavier Nady NYA |
| 29 | 342nd | SP Zach Duke Pit |