| Round | Overall | Player |
|---|---|---|
| 1 | 3rd | 3B Alex Rodriguez NYA |
| 2 | 22nd | OF Justin Upton Ari |
| 3 | 27th | OF Grady Sizemore Cle |
| 4 | 46th | SP Dan Haren LAA |
| 5 | 51st | SP Justin Verlander Det |
| 6 | 70th | 1B Billy Butler KC |
| 7 | 75th | 2B Brian Roberts Bal |
| 8 | 94th | 3B Aramis Ramirez ChN |
| 9 | 99th | RP Francisco Rodriguez NYN |
| 10 | 118th | RP Carlos Marmol ChN |
| 11 | 123rd | SP Brett Anderson Oak |
| 12 | 142nd | SP Carlos Zambrano ChN |
| 13 | 147th | OF Nate McLouth Atl |
| 14 | 166th | OF Carlos Beltran NYN |
| 15 | 171st | 1B Adam LaRoche Was |
| 16 | 190th | SS Rafael Furcal LAD |
| 17 | 195th | SP Wade Davis TB |
| 18 | 214th | C Yadier Molina StL |
| 19 | 219th | SP Joe Saunders Ari |
| 20 | 238th | OF Colby Rasmus StL |
| 21 | 243rd | SP Mat Latos SD |
| 22 | 262nd | SS Ryan Theriot STL |
| 23 | 267th | SP Ryan Madson Phi |
| 24 | 286th | C Ramon Hernandez Cin |
| 25 | 291st | SP C.J. Wilson Tex |
| 26 | 310th | 3B Albert Callaspo LAA |
| 27 | 315th | SP Nick Blackburn Min |
| 28 | 334th | OF Milton Bradley Sea |
| 29 | 339th | 3B Edwin Encarnacion Oak |