| Round | Overall | Player |
|---|---|---|
| 1 | 12th | OF Lance Berkman Hou |
| 2 | 13th | 2B Jeff Kent Hou |
| 3 | 36th | SP Roy Halladay Tor |
| 4 | 37th | OF Pat Burrell Phi |
| 5 | 60th | RP Troy Percival Ana |
| 6 | 61st | RP Kazuhiro Sasaki Sea |
| 7 | 84th | OF Bernie Williams NYA |
| 8 | 85th | SP A.J. Burnett Fla |
| 9 | 108th | SS David Eckstein Ana |
| 10 | 109th | SP Kevin Brown LA |
| 11 | 132nd | SP Tim Wakefield Bos |
| 12 | 133rd | 1B Mo Vaughn NYN |
| 13 | 156th | 3B Tony Batista Bal |
| 14 | 157th | SP Paul Byrd Atl |
| 15 | 180th | OF David Roberts LA |
| 16 | 181st | C Jason Varitek Bos |
| 17 | 204th | OF Tim Salmon Ana |
| 18 | 205th | 1B Fred McGriff LA |
| 19 | 228th | SP Johan Santana Min |
| 20 | 229th | SP Pedro Astacio NYN |
| 21 | 252nd | 3B Mark Bellhorn Col |
| 22 | 253rd | 1B Hee Seop Choi ChN |
| 23 | 276th | RP Mike DeJean StL |
| 24 | 277th | SP John Patterson Ari |
| 25 | 300th | 2B Mark Ellis Oak |
| 26 | 301st | SP Chuck Finley F/A |
| 27 | 324th | C Doug Mirabelli Bos |
| 28 | 325th | OF Carl Crawford TB |
| 29 | 348th | SP Brandon Duckworth Phi |