| Round | Overall | Player |
|---|---|---|
| 1 | 5th | 2B Robinson Cano NYA |
| 2 | 20th | OF Josh Hamilton LAA |
| 3 | 29th | SP Tim Lincecum SF |
| 4 | 44th | SP Cole Hamels Phi |
| 5 | 53rd | 3B Ryan Zimmerman Was |
| 6 | 68th | C Brian McCann Atl |
| 7 | 77th | SS J.J. Hardy Bal |
| 8 | 92nd | RP Jon Papelbon Phi |
| 9 | 101st | OF Carlos Beltran STL |
| 10 | 116th | RP Brian Wilson SF |
| 11 | 125th | SP Matt Garza ChN |
| 12 | 140th | 1B Carlos Lee Mia |
| 13 | 149th | SP Johan Santana NYN |
| 14 | 164th | 1B Logan Morrison Mia |
| 15 | 173rd | 1B Matt Gamel Mil |
| 16 | 188th | SP John Danks ChA |
| 17 | 197th | 3B Pedro Alvarez Pit |
| 18 | 212th | OF Josh Willingham Min |
| 19 | 221st | OF Matt Joyce TB |
| 20 | 236th | 2B Gordon Beckham ChA |
| 21 | 245th | SP Jonathan Sanchez Col |
| 22 | 260th | OF J.D. Martinez Hou |
| 23 | 269th | SS Clint Barmes Pit |
| 24 | 284th | C Rod Barajas Pit |
| 25 | 293rd | SP Bronson Arroyo Cin |
| 26 | 308th | RP Brad Peacock Oak |
| 27 | 317th | OF Manny Ramirez TB |
| 28 | 332nd | SP Billy Traber Bos |
| 29 | 341st | SP R.A. Dickey Tor |