| Round | Overall | Player |
|---|---|---|
| 1 | 12th | OF Ryan Braun Mil |
| 2 | 13th | OF Bryce Harper Was |
| 3 | 36th | SS Ian Desmond Was |
| 4 | 37th | SP Felix Hernandez Sea |
| 5 | 60th | OF Mark Trumbo Ari |
| 6 | 61st | 1B Anthony Rizzo ChN |
| 7 | 84th | OF Alexis Rios Tex |
| 8 | 85th | SP Cole Hamels Phi |
| 9 | 108th | SP Shelby Miller StL |
| 10 | 109th | 2B Brandon Phillips Cin |
| 11 | 132nd | SP Mike Minor Atl |
| 12 | 133rd | RP David Robertson NYA |
| 13 | 156th | 3B Kyle Seager Sea |
| 14 | 157th | SP Ervin Santana Atl |
| 15 | 180th | SP Michael Pineda NYA |
| 16 | 181st | SP Anthony Cingrani Cin |
| 17 | 204th | SP A.J. Burnett Phi |
| 18 | 205th | SP Matt Garza Mil |
| 19 | 228th | SS Starlin Castro ChN |
| 20 | 229th | OF Grady Sizemore Bos |
| 21 | 252nd | C A.J. Pierzynski StL |
| 22 | 253rd | C Mike Zunino Sea |
| 23 | 276th | RP Nathan Jones ChA |
| 24 | 277th | RP Bobby Parnell NYN |
| 25 | 300th | 1B Ike Davis Pit |
| 26 | 301st | 2B Brian Roberts NYA |
| 27 | 324th | 3B Cody Asche Phi |
| 28 | 325th | OF Michael Choice Tex |
| 29 | 348th | SP Ricky Nolasco Min |