| Round | Overall | Player |
|---|---|---|
| 1 | 9th | 1B Mark Teixeira NYA |
| 2 | 16th | 3B Ryan Zimmerman Was |
| 3 | 33rd | 3B Kevin Youkilis Bos |
| 4 | 40th | 2B Dan Uggla Atl |
| 5 | 57th | SP Dan Haren LAA |
| 6 | 64th | SP Chris Carpenter StL |
| 7 | 81st | RP Francisco Cordero Cin |
| 8 | 88th | OF Jacoby Ellsbury Bos |
| 9 | 105th | RP Jose Valverde Det |
| 10 | 112th | OF Nate McLouth Atl |
| 11 | 129th | SP Mark Buehrle ChA |
| 12 | 136th | OF Nick Swisher NYA |
| 13 | 153rd | SP Gavin Floyd ChA |
| 14 | 160th | OF Nolan Reimold Bal |
| 15 | 177th | SP Derek Lowe Atl |
| 16 | 184th | SS Rafael Furcal LAD |
| 17 | 201st | SP Andy Pettitte NYA |
| 18 | 208th | 1B Todd Helton Col |
| 19 | 225th | SP Bronson Arroyo Cin |
| 20 | 232nd | SS Orlando Cabrera Cin |
| 21 | 249th | SP Kevin Correia Pit |
| 22 | 256th | 2B Clint Barmes Col |
| 23 | 273rd | 3B Kevin Kouzmanoff Oak |
| 24 | 280th | C A.J. Pierzynski ChA |
| 25 | 297th | SS Alcides Escobar KC |
| 26 | 304th | SP Dallas Braden Oak |
| 27 | 321st | C Miguel Olivo Sea |
| 28 | 328th | OF Josh Willingham Was |
| 29 | 345th | OF Dexter Fowler Col |