| Round | Overall | Player |
|---|---|---|
| 1 | 6th | 1B Jeff Bagwell Hou |
| 2 | 19th | SP Randy Johnson Ari |
| 3 | 30th | RP Billy Wagner Hou |
| 4 | 43rd | 2B Jay Bell Ari |
| 5 | 54th | 3B Robin Ventura NYN |
| 6 | 67th | SS Tony Womack Ari |
| 7 | 78th | OF Jeromy Burnitz Mil |
| 8 | 91st | OF Gary Sheffield LA |
| 9 | 102nd | OF Moises Alou Hou |
| 10 | 115th | 2B Eric Young ChN |
| 11 | 126th | SP David Cone NYA |
| 12 | 139th | RP Todd Jones Det |
| 13 | 150th | 1B Kevin Young Pit |
| 14 | 163rd | OF Luis Gonzalez Ari |
| 15 | 174th | SP Aaron Sele Sea |
| 16 | 187th | RP Anthony Alford Fla |
| 17 | 198th | OF Jose Cruz Jr Tor |
| 18 | 211th | C Brad Ausmus Det |
| 19 | 222nd | SP Roy Halladay Tor |
| 20 | 235th | OF Ellis Burks SF |
| 21 | 246th | SP Andy Benes StL |
| 22 | 259th | SP Scott Erickson Bal |
| 23 | 270th | SP Sterling Hitchcock SD |
| 24 | 283rd | 3B Michael Barrett Mon |
| 25 | 294th | 1B Rico Brogna Phi |
| 26 | 307th | OF Steve Finley Ari |
| 27 | 318th | SP Kirk Rueter SF |