| Round | Overall | Player |
|---|---|---|
| 1 | 5th | OF Matt Holliday Col |
| 2 | 20th | OF Melvin Upton TB |
| 3 | 29th | 1B Lance Berkman Hou |
| 4 | 44th | SP Dan Haren Ari |
| 5 | 53rd | OF Manny Ramirez LAD |
| 6 | 68th | 3B Chone Figgins LAA |
| 7 | 77th | SP Francisco Liriano Min |
| 8 | 92nd | RP Mariano Rivera NYA |
| 9 | 101st | SP Tim Lincecum Hou |
| 10 | 116th | RP Rafael Soriano Atl |
| 11 | 125th | SP Philip Hughes NYA |
| 12 | 140th | OF Pat Burrell TB |
| 13 | 149th | DH Jim Thome ChA |
| 14 | 164th | RP Chad Cordero Was |
| 15 | 173rd | SP Clay Buchholz Bos |
| 16 | 188th | OF Justin Upton Ari |
| 17 | 197th | RP Eric Gagne Mil |
| 18 | 212th | SS Stephen Drew Ari |
| 19 | 221st | 3B Kevin Kouzmanoff SD |
| 20 | 236th | SP Gil Meche KC |
| 21 | 245th | 2B Mark Ellis Oak |
| 22 | 260th | 1B Conor Jackson Ari |
| 23 | 269th | 3B Bill Hall Mil |
| 24 | 284th | SP Greg Maddux SD |
| 25 | 293rd | SP Jair Jurrjens Atl |
| 26 | 308th | C Paul Lo Duca Was |
| 27 | 317th | 1B Casey Kotchman Atl |
| 28 | 332nd | C Chris Snyder Ari |
| 29 | 341st | OF Michael Bourn Hou |