| Round | Overall | Player |
|---|---|---|
| 1 | 8th | SP Clayton Kershaw LAD |
| 2 | 17th | 3B David Wright NYN |
| 3 | 32nd | OF Shin-Soo Choo Tex |
| 4 | 41st | SP Madison Bumgarner SF |
| 5 | 56th | 1B Mike Napoli Bos |
| 6 | 65th | OF Jayson Werth Was |
| 7 | 80th | OF Starling Marte Pit |
| 8 | 89th | RP Joe Nathan Det |
| 9 | 104th | OF Carlos Beltran NYA |
| 10 | 113th | SP Homer Bailey Cin |
| 11 | 128th | RP Koji Uehara Bos |
| 12 | 137th | SP Justin Masterson StL |
| 13 | 152nd | SS Jhonny Peralta StL |
| 14 | 161st | 2B Dan Murphy NYN |
| 15 | 176th | DH Adam Dunn ChA |
| 16 | 185th | SP Hiroki Kuroda NYA |
| 17 | 200th | SP Ubaldo Jimenez Bal |
| 18 | 209th | SP Tim Lincecum SF |
| 19 | 224th | C Jarrod Saltalamacchia Mia |
| 20 | 233rd | SS Derek Jeter NYA |
| 21 | 248th | C Yan Gomes Cle |
| 22 | 257th | 2B Omar Infante KC |
| 23 | 272nd | 1B James Loney TB |
| 24 | 281st | 3B David Freese LAA |
| 25 | 296th | SP Tyler Chatwood Col |
| 26 | 305th | OF Leonys Martin Tex |
| 27 | 320th | 1B Logan Morrison Sea |
| 28 | 329th | OF Daniel Nava Bos |
| 29 | 344th | SP Ryan Vogelsong SF |