| Round | Overall | Player |
|---|---|---|
| 1 | 7th | OF Manny Ramirez Bos |
| 2 | 18th | 1B Ryan Howard Phi |
| 3 | 31st | SP Roy Halladay Tor |
| 4 | 42nd | OF Carl Crawford TB |
| 5 | 55th | RP Joe Nathan Min |
| 6 | 66th | 3B Scott Rolen StL |
| 7 | 79th | SP John Smoltz Atl |
| 8 | 90th | SP Jason Schmidt SF |
| 9 | 103rd | RP B.J. Ryan Tor |
| 10 | 114th | C Ivan Rodriguez Det |
| 11 | 127th | OF Torii Hunter Min |
| 12 | 138th | RP Bobby Jenks ChA |
| 13 | 151st | SP Scott Kazmir TB |
| 14 | 162nd | 2B Ron Belliard StL |
| 15 | 175th | OF Randy Winn SF |
| 16 | 186th | RP Bob Wickman Atl |
| 17 | 199th | OF Jacque Jones ChN |
| 18 | 210th | 1B Lyle Overbay Tor |
| 19 | 223rd | 3B Mike Lowell Bos |
| 20 | 234th | SS Julio Lugo Bos |
| 21 | 247th | 3B Pedro Feliz SF |
| 22 | 258th | 1B Phil Nevin Min |
| 23 | 271st | 2B Orlando Hudson Ari |
| 24 | 282nd | SP Steve Trachsel NYN |
| 25 | 295th | C Yadier Molina StL |
| 26 | 306th | OF Xavier Nady Pit |
| 27 | 319th | SS Craig Counsell Ari |
| 28 | 330th | SP Rafael Soriano Sea |