| Round | Overall | Player |
|---|---|---|
| 1 | 12th | OF Curtis Granderson NYA |
| 2 | 13th | 2B Dustin Pedroia Bos |
| 3 | 36th | C Mike Napoli Bos |
| 4 | 37th | SP C.C. Sabathia NYA |
| 5 | 60th | 3B Brett Lawrie Tor |
| 6 | 61st | SP C.J. Wilson LAA |
| 7 | 84th | RP Jose Valverde Det |
| 8 | 85th | RP John Axford Mil |
| 9 | 108th | SP Doug Fister Det |
| 10 | 109th | OF Melky Cabrera Tor |
| 11 | 132nd | 1B Gaby Sanchez Pit |
| 12 | 133rd | 1B Corey Hart Mil |
| 13 | 156th | SP Tim Hudson Atl |
| 14 | 157th | 1B Carlos Pena TB |
| 15 | 180th | OF Delmon Young Det |
| 16 | 181st | SS Yunel Escobar TB |
| 17 | 204th | SP Brandon McCarthy Ari |
| 18 | 205th | C Geovany Soto Tex |
| 19 | 228th | SS Rafael Furcal STL |
| 20 | 229th | SP Drew Pomeranz Col |
| 21 | 252nd | OF Alex Presley Pit |
| 22 | 253rd | SP Matt Harrison Tex |
| 23 | 276th | SP Erik Bedard Pit |
| 24 | 277th | SS Mike Aviles Cle |
| 25 | 300th | 1B Casey Kotchman Cle |
| 26 | 301st | 2B Alexi Casilla Min |
| 27 | 324th | RP Jeff Karstens Pit |
| 28 | 325th | SP Kyle Lohse StL |
| 29 | 348th | 3B Alex Liddi Sea |