| Round | Overall | Player |
|---|---|---|
| 1 | 12th | OF Barry Bonds SF |
| 2 | 13th | C Jason Kendall Pit |
| 3 | 36th | 2B Chuck Knoblauch NYA |
| 4 | 37th | SS Edgar Renteria StL |
| 5 | 60th | 1B Frank Thomas ChA |
| 6 | 61st | RP Armando Benitez NYN |
| 7 | 84th | SP Shane Reynolds Hou |
| 8 | 85th | RP Robb Nen SF |
| 9 | 108th | OF Brian Jordan Atl |
| 10 | 109th | OF Moises Alou Hou |
| 11 | 132nd | SP Andy Ashby Phi |
| 12 | 133rd | 3B Travis Fryman Cle |
| 13 | 156th | 1B Richie Sexson Cle |
| 14 | 157th | OF Cliff Floyd Fla |
| 15 | 180th | SP Francisco Cordova Pit |
| 16 | 181st | SP Bruce Chen Atl |
| 17 | 204th | SP Scott Elarton Hou |
| 18 | 205th | SP Kip Wells ChA |
| 19 | 228th | SP Jon Lieber ChN |
| 20 | 229th | SP Steve Woodard Mil |
| 21 | 252nd | SP Andy Benes StL |
| 22 | 253rd | C Eli Marrero StL |
| 23 | 276th | 3B Mike Lowell Fla |
| 24 | 277th | RP Mike Williams Pit |
| 25 | 300th | 1B J.T. Snow SF |
| 26 | 301st | OF Richard Hidalgo Hou |
| 27 | 324th | SS Mark Loretta Mil |