| Round | Overall | Player |
|---|---|---|
| 1 | 3rd | 1B Ryan Howard Phi |
| 2 | 22nd | OF Matt Holliday StL |
| 3 | 27th | SP Roy Halladay Phi |
| 4 | 46th | SP Johan Santana NYN |
| 5 | 51st | SP Adam Wainwright StL |
| 6 | 70th | OF Josh Hamilton Tex |
| 7 | 75th | RP Jon Papelbon Bos |
| 8 | 94th | RP Brian Wilson SF |
| 9 | 99th | RP Andrew Bailey Oak |
| 10 | 118th | 2B Clint Barmes Col |
| 11 | 123rd | OF Carlos Gonzalez Col |
| 12 | 142nd | OF Raul Ibanez Phi |
| 13 | 147th | 3B David Freese StL |
| 14 | 166th | SS Alcides Escobar KC |
| 15 | 171st | C Ryan Doumit Pit |
| 16 | 190th | OF Dexter Fowler Col |
| 17 | 195th | 3B Martin Prado Atl |
| 18 | 214th | OF Jose Guillen SF |
| 19 | 219th | SP Randy Wolf Mil |
| 20 | 238th | SP Scott Kazmir LAA |
| 21 | 243rd | SP Stephen Strasburg Was |
| 22 | 262nd | OF Austin Jackson Det |
| 23 | 267th | SP Randy Wells ChN |
| 24 | 286th | SP Joe Saunders Ari |
| 25 | 291st | OF Brett Gardner NYA |
| 26 | 310th | OF Milton Bradley Sea |
| 27 | 315th | DH Pat Burrell SF |
| 28 | 334th | 3B Joe Crede Min |
| 29 | 339th | 1B Jason Giambi Col |