| Round | Overall | Player |
|---|---|---|
| 1 | 9th | OF Alfonso Soriano ChN |
| 2 | 16th | 3B Aramis Ramirez ChN |
| 3 | 33rd | OF Jason Bay NYN |
| 4 | 40th | C Geovany Soto ChN |
| 5 | 57th | SP Dan Haren Ari |
| 6 | 64th | 1B Derrek Lee ChN |
| 7 | 81st | SP Chad Billingsley LAD |
| 8 | 88th | SP John Danks ChA |
| 9 | 105th | SP Adam Wainwright StL |
| 10 | 112th | OF Brad Hawpe Col |
| 11 | 129th | RP Carlos Marmol ChN |
| 12 | 136th | SP Matt Garza TB |
| 13 | 153rd | SS Rafael Furcal LAD |
| 14 | 160th | RP Chad Qualls Ari |
| 15 | 177th | OF Mark DeRosa SF |
| 16 | 184th | OF Delmon Young Min |
| 17 | 201st | SP Brad Penny StL |
| 18 | 208th | SS Ryan Theriot ChN |
| 19 | 225th | 2B Orlando Hudson LAD |
| 20 | 232nd | RP Brandon Lyon Det |
| 21 | 249th | SP Kyle Lohse StL |
| 22 | 256th | 1B Mike Jacobs KC |
| 23 | 273rd | OF Coco Crisp Oak |
| 24 | 280th | OF Jeremy Hermida Bos |
| 25 | 297th | OF Josh Willingham Was |
| 26 | 304th | 3B Bill Hall Mil |
| 27 | 321st | RP Manuel Corpas Col |
| 28 | 328th | C John Buck KC |
| 29 | 345th | OF Willy Taveras Cin |