| Round | Overall | Player |
|---|---|---|
| 1 | 6th | SS Miguel Tejada Bal |
| 2 | 19th | OF Adam Dunn Cin |
| 3 | 30th | SP Jake Peavy SD |
| 4 | 43rd | SP Carlos Zambrano ChN |
| 5 | 54th | SP Felix Hernandez Sea |
| 6 | 67th | RP Huston Street Oak |
| 7 | 78th | 3B Adrian Beltre Sea |
| 8 | 91st | 1B Jason Giambi NYA |
| 9 | 102nd | SP Brandon Webb Ari |
| 10 | 115th | OF Jeff Francoeur Atl |
| 11 | 126th | SP Zach Duke Pit |
| 12 | 139th | 3B Edwin Encarnacion Cin |
| 13 | 150th | SP Francisco Liriano Min |
| 14 | 163rd | SP Matt Cain SF |
| 15 | 174th | OF Kevin Mench Mil |
| 16 | 187th | DH Javy Lopez Bos |
| 17 | 198th | OF Curtis Granderson Det |
| 18 | 211th | 2B Craig Biggio Hou |
| 19 | 222nd | SP Tim Wakefield Bos |
| 20 | 235th | 2B Placido Polanco Det |
| 21 | 246th | OF Raul Ibanez Sea |
| 22 | 259th | 1B Mike Jacobs Fla |
| 23 | 270th | RP Scott Baker Min |
| 24 | 283rd | OF Matt Murton ChN |
| 25 | 294th | SS Brandon Wood LAA |
| 26 | 307th | C Brian McCann Atl |
| 27 | 318th | RP Joe Borowski Cle |
| 28 | 331st | C Ryan Doumit Pit |