| Round | Overall | Player |
|---|---|---|
| 1 | 6th | 1B Ryan Howard Phi |
| 2 | 19th | SP Tim Lincecum SF |
| 3 | 30th | OF Matt Kemp LAD |
| 4 | 43rd | 3B Aramis Ramirez ChN |
| 5 | 54th | 2B Howie Kendrick LAA |
| 6 | 67th | RP Mariano Rivera NYA |
| 7 | 78th | OF Melvin Upton TB |
| 8 | 91st | SP Ricky Nolasco Fla |
| 9 | 102nd | RP Heath Bell SD |
| 10 | 115th | SP Jair Jurrjens Atl |
| 11 | 126th | SS Alexei Ramirez ChA |
| 12 | 139th | C Russell Martin NYA |
| 13 | 150th | OF Alexis Rios ChA |
| 14 | 163rd | SP Aaron Cook Col |
| 15 | 174th | SP Stephen Strasburg Was |
| 16 | 187th | SP Joel Pineiro LAA |
| 17 | 198th | OF Ryan Ludwick SD |
| 18 | 211th | SP Hiroki Kuroda LAD |
| 19 | 222nd | SS Ryan Theriot STL |
| 20 | 235th | C Yadier Molina StL |
| 21 | 246th | OF Alex Gordon KC |
| 22 | 259th | 3B Albert Callaspo LAA |
| 23 | 270th | 1B Ty Wigginton Col |
| 24 | 283rd | SP Justin Duchscherer Oak |
| 25 | 294th | OF Rajai Davis Oak |
| 26 | 307th | OF Juan Pierre ChA |
| 27 | 318th | SP Brad Mills Tor |
| 28 | 331st | OF Xavier Nady Ari |
| 29 | 342nd | SP Kei Igawa NYA |