| Round | Overall | Player |
|---|---|---|
| 1 | 2nd | SP Pedro Martinez Bos |
| 2 | 23rd | OF Barry Bonds SF |
| 3 | 26th | SP Kevin Brown LA |
| 4 | 47th | 1B Mark McGwire StL |
| 5 | 50th | 3B Jeff Cirillo Col |
| 6 | 71st | OF Bernie Williams NYA |
| 7 | 74th | C Javy Lopez Atl |
| 8 | 95th | SS Barry Larkin Cin |
| 9 | 98th | OF Jermaine Dye KC |
| 10 | 119th | 2B Luis Castillo Fla |
| 11 | 122nd | SP Jeff D'Amico Mil |
| 12 | 143rd | 1B Paul Konerko ChA |
| 13 | 146th | RP John Smoltz Atl |
| 14 | 167th | SP Brad Radke Min |
| 15 | 170th | SP Jarrod Washburn Ana |
| 16 | 191st | SP Carl Pavano Mon |
| 17 | 194th | SP Ramon Ortiz Ana |
| 18 | 215th | OF Steve Finley Ari |
| 19 | 218th | SP Shane Reynolds Hou |
| 20 | 239th | SP Sidney Ponson Bal |
| 21 | 242nd | 1B Tino Martinez NYA |
| 22 | 263rd | C Bobby Estalella SF |
| 23 | 266th | OF Gabe Kapler Tex |
| 24 | 287th | 3B Aaron Boone Cin |
| 25 | 290th | SS Mark Loretta Mil |
| 26 | 311th | SP Jim Parque ChA |
| 27 | 314th | RP Steve Karsay Cle |
| 28 | 335th | 2B Luis Rivas Min |
| 29 | 338th | SP Brian Tollberg SD |