| Round | Overall | Player |
|---|---|---|
| 1 | 5th | OF Barry Bonds SF |
| 2 | 20th | 1B Jim Thome Cle |
| 3 | 29th | P Randy Johnson Sea |
| 4 | 44th | OF Kenny Lofton Cle |
| 5 | 53rd | P Tom Glavine Atl |
| 6 | 68th | P Ismael Valdez LA |
| 7 | 77th | OF Rusty Greer Tex |
| 8 | 92nd | P Kevin Appier KC |
| 9 | 101st | 2B Ray Durham ChA |
| 10 | 116th | OF Paul O'Neill NYA |
| 11 | 125th | C Todd Greene Ana |
| 12 | 140th | P Andy Ashby SD |
| 13 | 149th | SS Jeff Blauser ChN |
| 14 | 164th | SS Miguel Tejada Oak |
| 15 | 173rd | OF Todd Helton Col |
| 16 | 188th | C Terry Steinbach Min |
| 17 | 197th | 3B Dave Hollins Ana |
| 18 | 212th | DH Chili Davis NYA |
| 19 | 221st | P Kirk Rueter SF |
| 20 | 236th | P Chris Holt Hou |
| 21 | 245th | OF Jeffrey Hammonds Bal |
| 22 | 260th | C Chris Hoiles Bal |
| 23 | 269th | 3B Fernando Tatis Tex |
| 24 | 284th | P Chad Ogea Cle |
| 25 | 293rd | OF Richard Hidalgo Hou |
| 26 | 308th | P Ramon Garcia Hou |
| 27 | 317th | 2B Jose Offerman KC |