| Round | Overall | Player |
|---|---|---|
| 1 | 7th | 2B Craig Biggio Hou |
| 2 | 18th | OF Ray Lankford StL |
| 3 | 31st | 1B Jim Thome Cle |
| 4 | 42nd | 3B Scott Rolen Phi |
| 5 | 55th | P Pat Hentgen Tor |
| 6 | 66th | P John Smoltz Atl |
| 7 | 79th | OF Rusty Greer Tex |
| 8 | 90th | P Justin Thompson Det |
| 9 | 103rd | P Mike Hampton Hou |
| 10 | 114th | P Joey Hamilton SD |
| 11 | 127th | 1B David Segui Sea |
| 12 | 138th | P Scott Erickson Bal |
| 13 | 151st | OF Eric Davis Bal |
| 14 | 162nd | SS Alex Gonzalez Tor |
| 15 | 175th | OF Henry Rodriguez ChN |
| 16 | 186th | P Carlos Perez Mon |
| 17 | 199th | C Todd Greene Ana |
| 18 | 210th | 3B Fernando Tatis Tex |
| 19 | 223rd | C Terry Steinbach Min |
| 20 | 234th | 1B Paul Konerko LA |
| 21 | 247th | P Darren Oliver Tex |
| 22 | 258th | P Kevin Tapani ChN |
| 23 | 271st | 1B Wally Joyner SD |
| 24 | 282nd | 2B Jose Offerman KC |
| 25 | 295th | P Scott Karl Mil |
| 26 | 306th | OF Chris Stynes Cin |
| 27 | 319th | OF Shannon Stewart Tor |