| Round | Overall | Player |
|---|---|---|
| 1 | 2nd | OF Barry Bonds SF |
| 2 | 23rd | 2B Jeff Kent Hou |
| 3 | 26th | 1B Carlos Delgado Tor |
| 4 | 47th | SP Wade Miller Hou |
| 5 | 50th | RP Billy Wagner Hou |
| 6 | 71st | OF Carlos Beltran KC |
| 7 | 74th | SP Matt Morris StL |
| 8 | 95th | RP Ugueth Urbina Fla |
| 9 | 98th | SP Jeff Weaver NYA |
| 10 | 119th | OF Tim Salmon Ana |
| 11 | 122nd | SP Hideo Nomo LA |
| 12 | 143rd | SS Rafael Furcal Atl |
| 13 | 146th | 3B Tony Batista Bal |
| 14 | 167th | OF Carlos Lee ChA |
| 15 | 170th | C Javy Lopez Atl |
| 16 | 191st | 1B Aubrey Huff TB |
| 17 | 194th | OF Kenny Lofton ChN |
| 18 | 215th | SS Tony Womack ChN |
| 19 | 218th | RP Brandon Villafuerte SD |
| 20 | 239th | C Damian Miller ChN |
| 21 | 242nd | SP Ismael Valdez Tex |
| 22 | 263rd | 2B Jerry Hairston Jr. Bal |
| 23 | 266th | 3B Craig Counsell Ari |
| 24 | 287th | 1B David Ortiz Bos |
| 25 | 290th | SP Chuck Finley F/A |
| 26 | 311th | SP Andy Ashby LA |
| 27 | 314th | OF David Roberts LA |
| 28 | 335th | SP John Patterson Ari |
| 29 | 338th | SP Jake Peavy SD |