| Round | Overall | Player |
|---|---|---|
| 1 | 6th | 1B Ryan Howard Phi |
| 2 | 19th | OF Adam Dunn Ari |
| 3 | 30th | DH Travis Hafner Cle |
| 4 | 43rd | OF Manny Ramirez LAD |
| 5 | 54th | OF Andruw Jones LAD |
| 6 | 67th | RP J.J. Putz Sea |
| 7 | 78th | 3B Chipper Jones Atl |
| 8 | 91st | 2B Rickie Weeks Mil |
| 9 | 102nd | SP Chris Young SD |
| 10 | 115th | SP John Maine NYN |
| 11 | 126th | SP Chad Billingsley LAD |
| 12 | 139th | SP Adam Wainwright StL |
| 13 | 150th | OF Raul Ibanez Sea |
| 14 | 163rd | SS Orlando Cabrera ChA |
| 15 | 174th | SP Bronson Arroyo Cin |
| 16 | 187th | RP Joakim Soria KC |
| 17 | 198th | SP Kevin Gregg Fla |
| 18 | 211th | 1B Daric Barton Oak |
| 19 | 222nd | 3B Kevin Kouzmanoff SD |
| 20 | 235th | SP Kenny Rogers Det |
| 21 | 246th | SP Johnny Cueto Cin |
| 22 | 259th | C A.J. Pierzynski ChA |
| 23 | 270th | 2B Mark Ellis Oak |
| 24 | 283rd | DH Frank Thomas Oak |
| 25 | 294th | SP C.J. Wilson Tex |
| 26 | 307th | SP Mike Hampton Atl |
| 27 | 318th | OF Jason Kubel Min |
| 28 | 331st | C Dioner Navarro TB |
| 29 | 342nd | SS Jack Wilson Pit |