| Round | Overall | Player |
|---|---|---|
| 1 | 5th | OF Barry Bonds SF |
| 2 | 20th | OF Ken Griffey Jr Cin |
| 3 | 29th | OF Juan Gonzalez Tex |
| 4 | 44th | SP Roger Clemens NYA |
| 5 | 53rd | 1B Richie Sexson Mil |
| 6 | 68th | SP Kevin Brown LA |
| 7 | 77th | SS Rafael Furcal Atl |
| 8 | 92nd | RP Ugueth Urbina Bos |
| 9 | 101st | 2B Jose Ortiz Col |
| 10 | 116th | SP Tom Glavine Atl |
| 11 | 125th | SP C.C. Sabathia Cle |
| 12 | 140th | 3B Sean Burroughs SD |
| 13 | 149th | OF Geoff Jenkins Mil |
| 14 | 164th | SP David Wells NYA |
| 15 | 173rd | 3B Aaron Boone Cin |
| 16 | 188th | RP Anthony Alford ChN |
| 17 | 197th | SP Juan Cruz ChN |
| 18 | 212th | SP Andy Ashby LA |
| 19 | 221st | 2B Adam Kennedy Ana |
| 20 | 236th | SS Julio Lugo Hou |
| 21 | 245th | SP Ismael Valdez Tex |
| 22 | 260th | C Raul Casanova Mil |
| 23 | 269th | 1B Steve Cox TB |
| 24 | 284th | SP Chuck Finley Cle |
| 25 | 293rd | OF Rusty Greer Tex |
| 26 | 308th | SP Erik Hiljus Oak |
| 27 | 317th | OF Steve Finley Ari |
| 28 | 332nd | 1B Erubiel Durazo Ari |
| 29 | 341st | OF Mark Quinn KC |