| Round | Overall | Player |
|---|---|---|
| 1 | 6th | OF Alfonso Soriano ChN |
| 2 | 19th | 3B Aramis Ramirez ChN |
| 3 | 30th | 2B Dan Uggla Fla |
| 4 | 43rd | C Geovany Soto ChN |
| 5 | 54th | SS Alexei Ramirez ChA |
| 6 | 67th | 1B Derrek Lee ChN |
| 7 | 78th | SP John Danks ChA |
| 8 | 91st | SP Adam Wainwright StL |
| 9 | 102nd | SP Zack Greinke KC |
| 10 | 115th | OF Brad Hawpe Col |
| 11 | 126th | SP Scott Baker Min |
| 12 | 139th | 3B Mark Reynolds Ari |
| 13 | 150th | SP Jair Jurrjens Atl |
| 14 | 163rd | SP Michael Pelfrey NYN |
| 15 | 174th | SP Andy Sonnanstine TB |
| 16 | 187th | RP Mike Gonzalez Atl |
| 17 | 198th | RP Brandon Lyon Det |
| 18 | 211th | RP Matt Capps Was |
| 19 | 222nd | 3B Miguel Tejada Bal |
| 20 | 235th | OF Coco Crisp Oak |
| 21 | 246th | RP Manuel Corpas Col |
| 22 | 259th | 1B Casey Kotchman Bos |
| 23 | 270th | 3B Placido Polanco Phi |
| 24 | 283rd | OF Xavier Nady ChN |
| 25 | 294th | OF Eric Byrnes Ari |
| 26 | 307th | OF Josh Willingham Was |
| 27 | 318th | 3B Bill Hall Mil |
| 28 | 331st | C Chris Snyder Ari |
| 29 | 342nd | OF Kosuke Fukudome ChN |