| Round | Overall | Player |
|---|---|---|
| 1 | 5th | SS Jose Reyes NYN |
| 2 | 20th | SP Brandon Webb Ari |
| 3 | 29th | 3B Aramis Ramirez ChN |
| 4 | 44th | SP Justin Verlander Det |
| 5 | 53rd | 1B Paul Konerko ChA |
| 6 | 68th | SP Chien-Ming Wang NYA |
| 7 | 77th | OF Hideki Matsui NYA |
| 8 | 92nd | 2B Kelly Johnson Atl |
| 9 | 101st | SS Miguel Tejada Hou |
| 10 | 116th | OF Jeff Francoeur Atl |
| 11 | 125th | SP Dustin McGowan Tor |
| 12 | 140th | SP Scott Kazmir TB |
| 13 | 149th | SP Philip Hughes NYA |
| 14 | 164th | RP Rafael Soriano Atl |
| 15 | 173rd | RP Brandon Lyon Det |
| 16 | 188th | OF Chris Duncan StL |
| 17 | 197th | RP Eric Gagne Mil |
| 18 | 212th | OF Johnny Damon NYA |
| 19 | 221st | OF Josh Willingham Fla |
| 20 | 236th | C Ben Molina SF |
| 21 | 245th | OF Michael Cuddyer Min |
| 22 | 260th | C Ronny Paulino Pit |
| 23 | 269th | 1B Mike Jacobs Fla |
| 24 | 284th | 3B Jose Bautista Pit |
| 25 | 293rd | SS Ryan Theriot ChN |
| 26 | 308th | SP Scott Baker Min |
| 27 | 317th | SP Micah Owings Ari |
| 28 | 332nd | 2B Tadahito Iguchi SD |
| 29 | 341st | RP Derrick Turnbow Mil |