| Round | Overall | Player |
|---|---|---|
| 1 | 6th | 1B Jeff Bagwell Hou |
| 2 | 19th | 2B Edgardo Alfonzo NYN |
| 3 | 30th | OF Brian S. Giles Pit |
| 4 | 43rd | RP Derek Lowe Bos |
| 5 | 54th | OF Richard Hidalgo Hou |
| 6 | 67th | SP Al Leiter NYN |
| 7 | 78th | SP Livan Hernandez SF |
| 8 | 91st | RP John Smoltz Atl |
| 9 | 102nd | OF Geoff Jenkins Mil |
| 10 | 115th | SP Ryan Dempster Fla |
| 11 | 126th | C Charles Johnson Fla |
| 12 | 139th | SP Jeff D'Amico Mil |
| 13 | 150th | OF Bob Higginson Det |
| 14 | 163rd | SP Matt Morris StL |
| 15 | 174th | SP Pete Harnisch Cin |
| 16 | 187th | 3B Travis Fryman Cle |
| 17 | 198th | RP Jose Jimenez Col |
| 18 | 211th | 2B Jose Offerman Bos |
| 19 | 222nd | OF Rusty Greer Tex |
| 20 | 235th | OF Jose Valentin ChA |
| 21 | 246th | DH Jose Canseco Ana |
| 22 | 259th | SS Ricky Gutierrez ChN |
| 23 | 270th | SP Frank Castillo Bos |
| 24 | 283rd | SS Mark Loretta Mil |
| 25 | 294th | RP Mike Williams Pit |
| 26 | 307th | SP Ismael Valdez Ana |
| 27 | 318th | 1B Rico Brogna Atl |
| 28 | 331st | 3B Jose Hernandez Mil |
| 29 | 342nd | C Sandy Alomar Jr. ChA |