| Round | Overall | Player |
|---|---|---|
| 1 | 12th | OF Ryan Braun Mil |
| 2 | 13th | 2B Dustin Pedroia Bos |
| 3 | 36th | OF Jay Bruce Cin |
| 4 | 37th | 3B Ryan Zimmerman Was |
| 5 | 60th | OF Shin-Soo Choo Cin |
| 6 | 61st | SP Jon Lester Bos |
| 7 | 84th | SS Jimmy Rollins Phi |
| 8 | 85th | SP Daniel Hudson Ari |
| 9 | 108th | RP Joel Hanrahan Bos |
| 10 | 109th | RP Brian Wilson SF |
| 11 | 132nd | 1B Justin Morneau Min |
| 12 | 133rd | 1B Logan Morrison Mia |
| 13 | 156th | SP Max Scherzer Det |
| 14 | 157th | SP Brandon Beachy Atl |
| 15 | 180th | RP Huston Street SD |
| 16 | 181st | SP Vance Worley Min |
| 17 | 204th | SP Colby Lewis Tex |
| 18 | 205th | 2B Aaron Hill Ari |
| 19 | 228th | SP Mike Leake Cin |
| 20 | 229th | 1B Matt Gamel Mil |
| 21 | 252nd | SP Ryan Dempster Bos |
| 22 | 253rd | OF Peter Bourjos LAA |
| 23 | 276th | C Ryan Doumit Min |
| 24 | 277th | SS Sean Rodriguez TB |
| 25 | 300th | 3B Ian Stewart ChN |
| 26 | 301st | OF Jason Kubel Ari |
| 27 | 324th | C Nick Hundley SD |
| 28 | 325th | 1B Brandon Allen TB |
| 29 | 348th | 1B Aubrey Huff SF |