| Round | Overall | Player |
|---|---|---|
| 1 | 12th | SS Derek Jeter NYA |
| 2 | 13th | 1B Jeff Bagwell Hou |
| 3 | 36th | P Mariano Rivera NYA |
| 4 | 37th | 2B Chuck Knoblauch NYA |
| 5 | 60th | P Billy Wagner Hou |
| 6 | 61st | OF Ray Lankford StL |
| 7 | 84th | OF Greg Vaughn Cin |
| 8 | 85th | C Jorge Posada NYA |
| 9 | 108th | 3B John Valentin Bos |
| 10 | 109th | OF Paul O'Neill NYA |
| 11 | 132nd | P Jeff Fassero Sea |
| 12 | 133rd | P John Franco NYN |
| 13 | 156th | 1B Mark Grace ChN |
| 14 | 157th | P Kenny Rogers Oak |
| 15 | 180th | 2B Jay Bell Ari |
| 16 | 181st | P Kelvim Escobar Tor |
| 17 | 204th | OF Brian S. Giles Pit |
| 18 | 205th | P Juan Acevedo StL |
| 19 | 228th | P Brian Moehler Det |
| 20 | 229th | OF Jeremy Giambi KC |
| 21 | 252nd | C Scott Hatteberg Bos |
| 22 | 253rd | OF Ron Gant Phi |
| 23 | 276th | P Steve Trachsel ChN |
| 24 | 277th | SS Alex Gonzalez Fla |
| 25 | 300th | 2B Carlos Febles KC |
| 26 | 301st | P Jon Lieber ChN |
| 27 | 324th | P Ramiro Mendoza NYA |