| Round | Overall | Player |
|---|---|---|
| 1 | 5th | C Mike Piazza NYN |
| 2 | 20th | 1B Mark McGwire StL |
| 3 | 29th | SP Greg Maddux Atl |
| 4 | 44th | OF Brian S. Giles Pit |
| 5 | 53rd | SP Roger Clemens NYA |
| 6 | 68th | 3B Dean Palmer Det |
| 7 | 77th | RP Jeff Shaw LA |
| 8 | 92nd | SP David Cone NYA |
| 9 | 101st | OF Moises Alou Hou |
| 10 | 116th | SP Tim Hudson Oak |
| 11 | 125th | OF Carlos Beltran KC |
| 12 | 140th | SS Rich Aurilia SF |
| 13 | 149th | OF Roger Cedeno Hou |
| 14 | 164th | 1B John Olerud Sea |
| 15 | 173rd | SP Rick Ankiel StL |
| 16 | 188th | 3B Troy Glaus Ana |
| 17 | 197th | SP Steve Woodard Mil |
| 18 | 212th | 2B Warren Morris Pit |
| 19 | 221st | OF Garret Anderson Ana |
| 20 | 236th | SP Paul Byrd Phi |
| 21 | 245th | SS Pat Meares Pit |
| 22 | 260th | SP Dave Mlicki Det |
| 23 | 269th | C Mitch Meluskey Hou |
| 24 | 284th | RP Ramiro Mendoza NYA |
| 25 | 293rd | OF Steve Finley Ari |
| 26 | 308th | OF Carlos Lee ChA |
| 27 | 317th | SP Bobby J. Jones NYN |