| Round | Overall | Player |
|---|---|---|
| 1 | 3rd | 1B Mark McGwire StL |
| 2 | 22nd | 1B Rafael Palmeiro Tex |
| 3 | 27th | OF Bernie Williams NYA |
| 4 | 46th | OF Bobby Abreu Phi |
| 5 | 51st | OF Raul Mondesi Tor |
| 6 | 70th | OF Carlos Beltran KC |
| 7 | 75th | 3B Robin Ventura NYN |
| 8 | 94th | SP Roger Clemens NYA |
| 9 | 99th | SS Edgar Renteria StL |
| 10 | 118th | SP David Cone NYA |
| 11 | 123rd | SP Andy Pettitte NYA |
| 12 | 142nd | OF Doug Glanville Phi |
| 13 | 147th | 2B Homer Bush Tor |
| 14 | 166th | C Darrin Fletcher Tor |
| 15 | 171st | 3B Joe Randa KC |
| 16 | 190th | SP Pat Hentgen StL |
| 17 | 195th | SP Octavio Dotel Hou |
| 18 | 214th | SP Kerry Wood ChN |
| 19 | 219th | RP Jason Isringhausen Oak |
| 20 | 238th | OF Roger Cedeno Hou |
| 21 | 243rd | 1B Mark Grace ChN |
| 22 | 262nd | RP Ricky Bottalico KC |
| 23 | 267th | RP Anthony Alford Fla |
| 24 | 286th | SP Ed Yarnall NYA |
| 25 | 291st | C Eli Marrero StL |
| 26 | 310th | OF Bob Higginson Det |
| 27 | 315th | RP Orber Moreno KC |