| Round | Overall | Player |
|---|---|---|
| 1 | 4th | OF Matt Kemp LAD |
| 2 | 21st | SS Jose Reyes Tor |
| 3 | 28th | OF Josh Hamilton LAA |
| 4 | 45th | SP Tim Lincecum SF |
| 5 | 52nd | 3B David Wright NYN |
| 6 | 69th | SP Stephen Strasburg Was |
| 7 | 76th | SP Madison Bumgarner SF |
| 8 | 93rd | C Matt Wieters Bal |
| 9 | 100th | OF Andre Ethier LAD |
| 10 | 117th | DH David Ortiz Bos |
| 11 | 124th | 2B Howie Kendrick LAA |
| 12 | 141st | SP Doug Fister Det |
| 13 | 148th | 1B Freddie Freeman Atl |
| 14 | 165th | SP Hiroki Kuroda NYA |
| 15 | 172nd | RP Joe Nathan Tex |
| 16 | 189th | SP Ubaldo Jimenez Cle |
| 17 | 196th | OF Jayson Werth Was |
| 18 | 213th | SP Michael Pineda NYA |
| 19 | 220th | RP Kyle Farnsworth TB |
| 20 | 237th | 1B Yonder Alonso SD |
| 21 | 244th | SS Stephen Drew Bos |
| 22 | 261st | C Geovany Soto Tex |
| 23 | 268th | SP Roy Oswalt Tex |
| 24 | 285th | 2B Johnny Giavotella KC |
| 25 | 292nd | SP Edwin Jackson ChN |
| 26 | 309th | OF J.D. Martinez Hou |
| 27 | 316th | 3B Chris Johnson Ari |
| 28 | 333rd | RP Daniel Bard Bos |
| 29 | 340th | RP Brad Lidge Was |