| Round | Overall | Player |
|---|---|---|
| 1 | 3rd | OF Ryan Braun Mil |
| 2 | 22nd | SP Clayton Kershaw LAD |
| 3 | 27th | SP Roy Halladay Phi |
| 4 | 46th | 3B David Wright NYN |
| 5 | 51st | SP Matt Cain SF |
| 6 | 70th | SP Yovani Gallardo Mil |
| 7 | 75th | C Joe Mauer Min |
| 8 | 94th | 1B Michael Cuddyer Col |
| 9 | 99th | DH David Ortiz Bos |
| 10 | 118th | SS Derek Jeter NYA |
| 11 | 123rd | 1B Freddie Freeman Atl |
| 12 | 142nd | RP Jason Motte StL |
| 13 | 147th | 2B Neil Walker Pit |
| 14 | 166th | RP Drew Storen Was |
| 15 | 171st | SP Jordan Zimmermann Was |
| 16 | 190th | OF Lucas Duda NYN |
| 17 | 195th | SS Erick Aybar LAA |
| 18 | 214th | 2B Aaron Hill Ari |
| 19 | 219th | OF Dexter Fowler Col |
| 20 | 238th | SP Edwin Jackson ChN |
| 21 | 243rd | SP Chris Carpenter StL |
| 22 | 262nd | SP Ricky Nolasco Mia |
| 23 | 267th | 3B Danny Valencia Min |
| 24 | 286th | OF Angel Pagan SF |
| 25 | 291st | 1B Mitch Moreland Tex |
| 26 | 310th | SP Grant Balfour Oak |
| 27 | 315th | C Miguel Olivo Sea |
| 28 | 334th | SP Bud Norris Hou |
| 29 | 339th | OF Marlon Byrd Bos |