| Round | Overall | Player |
|---|---|---|
| 1 | 6th | 1B Joey Votto Cin |
| 2 | 19th | OF Justin Upton Ari |
| 3 | 30th | 3B Brett Lawrie Tor |
| 4 | 43rd | SP Cole Hamels Phi |
| 5 | 54th | SP David Price TB |
| 6 | 67th | SP Ricky Romero Tor |
| 7 | 78th | SP Adam Wainwright StL |
| 8 | 91st | DH Adam Dunn ChA |
| 9 | 102nd | RP Jon Papelbon Phi |
| 10 | 115th | SS Derek Jeter NYA |
| 11 | 126th | C Miguel Montero Ari |
| 12 | 139th | OF Nick Swisher Cle |
| 13 | 150th | 2B Neil Walker Pit |
| 14 | 163rd | RP Sergio Santos Tor |
| 15 | 174th | OF Vernon Wells LAA |
| 16 | 187th | SP Colby Lewis Tex |
| 17 | 198th | SS Dee Strange-Gordon LAD |
| 18 | 211th | 1B Brandon Belt SF |
| 19 | 222nd | SP Jeremy Guthrie KC |
| 20 | 235th | OF Jason Kubel Ari |
| 21 | 246th | 2B Marcos Scutaro SF |
| 22 | 259th | RP Matt Capps Min |
| 23 | 270th | SP R.A. Dickey Tor |
| 24 | 283rd | C Wilson Ramos Was |
| 25 | 294th | RP Jonathan Broxton Cin |
| 26 | 307th | 3B Wilson Betemit Bal |
| 27 | 318th | SP Jeff Niemann TB |
| 28 | 331st | OF Coco Crisp Oak |
| 29 | 342nd | RP Greg Holland KC |