| Round | Overall | Player |
|---|---|---|
| 1 | 10th | C Ivan Rodriguez Tex |
| 2 | 15th | OF Barry Bonds SF |
| 3 | 34th | SS Rich Aurilia SF |
| 4 | 39th | 3B Scott Rolen Phi |
| 5 | 58th | 2B Bret Boone Sea |
| 6 | 63rd | 1B Jim Thome Cle |
| 7 | 82nd | SP Jon Lieber ChN |
| 8 | 87th | RP Anthony Alford ChN |
| 9 | 106th | OF Moises Alou ChN |
| 10 | 111th | SP Roy Halladay Tor |
| 11 | 130th | SP Mark Prior ChN |
| 12 | 135th | RP Byung-Hyun Kim Ari |
| 13 | 154th | OF Garret Anderson Ana |
| 14 | 159th | SP Brandon Duckworth Phi |
| 15 | 178th | SP Derek Lowe Bos |
| 16 | 183rd | SP Juan Cruz ChN |
| 17 | 202nd | SP John Burkett Bos |
| 18 | 207th | OF Delino DeShields ChN |
| 19 | 226th | OF Reggie Sanders SF |
| 20 | 231st | OF Ben Grieve TB |
| 21 | 250th | SP Dustin Hermanson Bos |
| 22 | 255th | C Todd Hundley ChN |
| 23 | 274th | 3B Shea Hillenbrand Bos |
| 24 | 279th | SS Jose Hernandez Mil |
| 25 | 298th | 2B Ricky Gutierrez Cle |
| 26 | 303rd | 1B Mark Grace Ari |
| 27 | 322nd | OF Doug Glanville Phi |
| 28 | 327th | SS Adam Everett Hou |
| 29 | 346th | SP Albie Lopez Atl |