| Round | Overall | Player |
|---|---|---|
| 1 | 9th | 1B David Ortiz Bos |
| 2 | 16th | SS Miguel Tejada Bal |
| 3 | 33rd | 1B Todd Helton Col |
| 4 | 40th | 3B Hank Blalock Tex |
| 5 | 57th | OF Carlos Beltran NYN |
| 6 | 64th | 2B Rickie Weeks Mil |
| 7 | 81st | RP Francisco Rodriguez LAA |
| 8 | 88th | RP Joe Nathan Min |
| 9 | 105th | SP Randy Johnson NYA |
| 10 | 112th | SP John Smoltz Atl |
| 11 | 129th | OF Jason Lane Hou |
| 12 | 136th | 3B Chad Tracy Ari |