| Round | Overall | Player |
|---|---|---|
| 1 | 2nd | 1B Albert Pujols StL |
| 2 | 23rd | OF Alfonso Soriano ChA |
| 3 | 26th | C Victor Martinez Cle |
| 4 | 47th | SS Jose Reyes NYN |
| 5 | 50th | SP Carlos Zambrano ChN |
| 6 | 71st | 3B Troy Glaus Tor |
| 7 | 74th | SS Jimmy Rollins Phi |
| 8 | 95th | 3B Chipper Jones Atl |
| 9 | 98th | SP Zach Duke Pit |
| 10 | 119th | OF Brad Wilkerson Tex |
| 11 | 122nd | SP Mark Prior ChN |
| 12 | 143rd | SP Francisco Liriano Min |
| 13 | 146th | OF Jeremy Hermida Fla |
| 14 | 167th | SP Jose Contreras ChA |
| 15 | 170th | C Michael Barrett ChN |
| 16 | 191st | 3B Edwin Encarnacion Cin |
| 17 | 194th | OF Curtis Granderson Det |
| 18 | 215th | SP Odalis Perez KC |
| 19 | 218th | 2B Mark Ellis Oak |
| 20 | 239th | 1B Conor Jackson Ari |
| 21 | 242nd | SP Justin Verlander Det |
| 22 | 263rd | SP Jason Marquis ChA |
| 23 | 266th | OF Delmon Young TB |
| 24 | 287th | SP Chien-Ming Wang NYA |
| 25 | 290th | OF Nick Markakis Bal |
| 26 | 311th | 2B Aaron Hill Tor |
| 27 | 314th | OF Jason Kubel Min |
| 28 | 335th | 3B Andy Marte Cle |
| 29 | 338th | 3B Joel Guzman LAD |