| Round | Overall | Player |
|---|---|---|
| 1 | 12th | 2B Dustin Pedroia Bos |
| 2 | 13th | OF Ryan Braun Mil |
| 3 | 36th | OF Jay Bruce Cin |
| 4 | 37th | OF Matt Holliday StL |
| 5 | 60th | SP Jon Lester Bos |
| 6 | 61st | OF Shin-Soo Choo Cin |
| 7 | 84th | SS J.J. Hardy Bal |
| 8 | 85th | 1B Ike Davis NYN |
| 9 | 108th | RP Brian Wilson SF |
| 10 | 109th | DH David Ortiz Bos |
| 11 | 132nd | RP Jason Motte StL |
| 12 | 133rd | 3B Mike Moustakas KC |
| 13 | 156th | 1B Carlos Pena TB |
| 14 | 157th | RP Joel Hanrahan Bos |
| 15 | 180th | OF Brennan Boesch Det |
| 16 | 181st | SP John Danks ChA |
| 17 | 204th | SP Trevor Cahill Ari |
| 18 | 205th | 2B Jemile Weeks Oak |
| 19 | 228th | SP Matt Harrison Tex |
| 20 | 229th | SS Stephen Drew Bos |
| 21 | 252nd | SP Henderson Alvarez Tor |
| 22 | 253rd | SP Ryan Dempster Bos |
| 23 | 276th | 3B Ian Stewart ChN |
| 24 | 277th | 1B Ty Wigginton Phi |
| 25 | 300th | C Chris Iannetta LAA |
| 26 | 301st | SP Mike Leake Cin |
| 27 | 324th | SP Ted Lilly LAD |
| 28 | 325th | C Ramon Hernandez Col |
| 29 | 348th | OF Josh Reddick Oak |