| Round | Overall | Player |
|---|---|---|
| 1 | 6th | 2B Chase Utley Phi |
| 2 | 19th | 1B Lance Berkman Hou |
| 3 | 30th | SP Brandon Webb Ari |
| 4 | 43rd | 3B Chipper Jones Atl |
| 5 | 54th | OF Melvin Upton TB |
| 6 | 67th | SP John Lackey Bos |
| 7 | 78th | SS Derek Jeter NYA |
| 8 | 91st | SP Zack Greinke KC |
| 9 | 102nd | C Chris Iannetta Col |
| 10 | 115th | RP Bobby Jenks ChA |
| 11 | 126th | RP Francisco Cordero Cin |
| 12 | 139th | OF Milton Bradley Sea |
| 13 | 150th | OF Justin Upton Ari |
| 14 | 163rd | 1B Conor Jackson Ari |
| 15 | 174th | SP Chris Young SD |
| 16 | 187th | SP Aaron Harang Cin |
| 17 | 198th | OF J.D. Drew Bos |
| 18 | 211th | SP Aaron Cook Col |
| 19 | 222nd | DH Jim Thome Min |
| 20 | 235th | SP Jesse Litsch Tor |
| 21 | 246th | 3B Joe Crede Min |
| 22 | 259th | 2B Akinori Iwamura Pit |
| 23 | 270th | C Dioner Navarro TB |
| 24 | 283rd | SP Ian Snell Pit |
| 25 | 294th | DH Gary Sheffield NYN |
| 26 | 307th | RP George Sherrill LAD |
| 27 | 318th | SP John Lannan Was |
| 28 | 331st | OF Ryan Church Pit |
| 29 | 342nd | SS Yuniesky Betancourt Sea |