| Round | Overall | Player |
|---|---|---|
| 1 | 5th | 1B Ryan Howard Phi |
| 2 | 20th | OF Matt Holliday StL |
| 3 | 29th | SP Roy Halladay Tor |
| 4 | 44th | RP Francisco Rodriguez NYN |
| 5 | 53rd | C Joe Mauer Min |
| 6 | 68th | SP Daisuke Matsuzaka Bos |
| 7 | 77th | SS Stephen Drew Ari |
| 8 | 92nd | 3B Jorge Cantu Fla |
| 9 | 101st | OF Jermaine Dye ChA |
| 10 | 116th | SP Ryan Dempster ChN |
| 11 | 125th | SP Ervin Santana LAA |
| 12 | 140th | 2B Kelly Johnson Ari |
| 13 | 149th | DH Pat Burrell TB |
| 14 | 164th | RP Matt Capps Was |
| 15 | 173rd | 1B Carlos Guillen Det |
| 16 | 188th | OF Elijah Dukes Was |
| 17 | 197th | RP Mike Gonzalez Atl |
| 18 | 212th | 3B Placido Polanco Phi |
| 19 | 221st | SS Yunel Escobar Atl |
| 20 | 236th | 3B Kevin Kouzmanoff Oak |
| 21 | 245th | SP Justin Duchscherer Oak |
| 22 | 260th | 1B Troy Glaus Atl |
| 23 | 269th | DH Hideki Matsui LAA |
| 24 | 284th | SP Bronson Arroyo Cin |
| 25 | 293rd | OF Chris Dickerson Cin |
| 26 | 308th | C Gerald Laird Det |
| 27 | 317th | C Chris Snyder Ari |
| 28 | 332nd | OF Kosuke Fukudome ChN |
| 29 | 341st | SP Zach Duke Pit |