| Round | Overall | Player |
|---|---|---|
| 1 | 9th | 1B Mark McGwire StL |
| 2 | 16th | OF Juan Gonzalez Det |
| 3 | 33rd | SP Kevin Brown LA |
| 4 | 40th | 2B Jeff Kent SF |
| 5 | 57th | SP Mike Mussina Bal |
| 6 | 64th | RP Billy Koch Tor |
| 7 | 81st | RP Mike Jackson Phi |
| 8 | 88th | 1B Andres Galarraga Atl |
| 9 | 105th | 3B Troy Glaus Ana |
| 10 | 112th | SP Curt Schilling Phi |
| 11 | 129th | OF Cliff Floyd Fla |
| 12 | 136th | SP Chuck Finley Cle |
| 13 | 153rd | SP Tim Hudson Oak |
| 14 | 160th | SP Jose Rosado KC |
| 15 | 177th | SP Kerry Wood ChN |
| 16 | 184th | OF Troy O'Leary Bos |
| 17 | 201st | SP Sidney Ponson Bal |
| 18 | 208th | OF B.J. Surhoff Bal |
| 19 | 225th | SS Rich Aurilia SF |
| 20 | 232nd | C Sandy Alomar Jr. Cle |
| 21 | 249th | SP Javier Vazquez Mon |
| 22 | 256th | OF Henry Rodriguez ChN |
| 23 | 273rd | C John Flaherty TB |
| 24 | 280th | SP Kelvim Escobar Tor |
| 25 | 297th | 1B Lee Stevens Mon |
| 26 | 304th | 2B David Bell Sea |
| 27 | 321st | 3B Shane Andrews ChN |