| Round | Overall | Player |
|---|---|---|
| 1 | 6th | SP Johan Santana Min |
| 2 | 19th | OF Carl Crawford TB |
| 3 | 30th | 3B Chone Figgins LAA |
| 4 | 43rd | SS Jimmy Rollins Phi |
| 5 | 54th | SP Chris Carpenter StL |
| 6 | 67th | OF Juan Pierre LAD |
| 7 | 78th | SP Ben Sheets Mil |
| 8 | 91st | OF Scott Podsednik ChA |
| 9 | 102nd | 2B Tadahito Iguchi ChA |
| 10 | 115th | SP A.J. Burnett Tor |
| 11 | 126th | SP John Lackey LAA |
| 12 | 139th | DH Javy Lopez Bos |
| 13 | 150th | SP Jose Contreras ChA |
| 14 | 163rd | SP Esteban Loaiza Oak |
| 15 | 174th | SP Jon Lieber Phi |
| 16 | 187th | C Kenji Johjima Sea |
| 17 | 198th | 1B Sean Casey Det |
| 18 | 211th | SP Miguel Batista Ari |
| 19 | 222nd | OF Jay Gibbons Bal |
| 20 | 235th | SP Aaron Harang Cin |
| 21 | 246th | SP Gustavo Chacin Tor |
| 22 | 259th | OF Raul Ibanez Sea |
| 23 | 270th | 1B Adam LaRoche Pit |
| 24 | 283rd | SP Adam Eaton Phi |
| 25 | 294th | 2B Ray Durham SF |
| 26 | 307th | 3B Melvin Upton TB |
| 27 | 318th | OF Brady Clark Mil |
| 28 | 331st | 3B Corey Koskie Mil |
| 29 | 342nd | C Brian Schneider Was |