| Round | Overall | Player |
|---|---|---|
| 1 | 6th | SS Jose Reyes NYN |
| 2 | 19th | OF Grady Sizemore Cle |
| 3 | 30th | C Brian McCann Atl |
| 4 | 43rd | SP Chris Carpenter StL |
| 5 | 54th | SP Brandon Webb Ari |
| 6 | 67th | OF Nick Swisher ChA |
| 7 | 78th | 3B Ryan Zimmerman Was |
| 8 | 91st | 3B Bill Hall Mil |
| 9 | 102nd | 1B Adam LaRoche Pit |
| 10 | 115th | RP Tom Gordon Phi |
| 11 | 126th | SP Chris Young SD |
| 12 | 139th | SP Anibal Sanchez Fla |
| 13 | 150th | OF Mark Teahen KC |
| 14 | 163rd | DH Frank Thomas Tor |
| 15 | 174th | SP Anthony Reyes StL |
| 16 | 187th | 2B Tadahito Iguchi Phi |
| 17 | 198th | SP Jeremy Sowers Cle |
| 18 | 211th | 1B Kevin Youkilis Bos |
| 19 | 222nd | SS Khalil Greene SD |
| 20 | 235th | RP Clay Hensley SD |
| 21 | 246th | SP Bartolo Colon LAA |
| 22 | 259th | OF Eric Byrnes Ari |
| 23 | 270th | SP Gustavo Chacin Tor |
| 24 | 283rd | C Miguel Olivo Fla |
| 25 | 294th | OF Josh Hamilton Tex |
| 26 | 307th | OF David DeJesus KC |
| 27 | 318th | 2B Jose Valentin NYN |
| 28 | 331st | SP Homer Bailey Cin |
| 29 | 342nd | SP Sidney Ponson Min |