| Round | Overall | Player |
|---|---|---|
| 1 | 12th | OF Barry Bonds SF |
| 2 | 13th | OF Larry Walker Col |
| 3 | 36th | 2B Jeff Kent SF |
| 4 | 37th | 1B Frank Thomas ChA |
| 5 | 60th | DH Jose Canseco TB |
| 6 | 61st | OF Magglio Ordonez ChA |
| 7 | 84th | 3B Adrian Beltre LA |
| 8 | 85th | C Eddie Taubensee Cin |
| 9 | 108th | SP Al Leiter NYN |
| 10 | 109th | SP Tim Hudson Oak |
| 11 | 132nd | SP David Cone NYA |
| 12 | 133rd | SP Omar Daal Ari |
| 13 | 156th | SP Chuck Finley Cle |
| 14 | 157th | OF Corey Patterson ChN |
| 15 | 180th | SS Jose Hernandez Mil |
| 16 | 181st | SP Kent Bottenfield Ana |
| 17 | 204th | SP Pedro Astacio Col |
| 18 | 205th | SP Chris Carpenter Tor |
| 19 | 228th | C Charles Johnson Bal |
| 20 | 229th | OF Carlos Lee ChA |
| 21 | 252nd | 2B Carlos Guillen Sea |
| 22 | 253rd | SP Javier Vazquez Mon |
| 23 | 276th | SP Juan Guzman TB |
| 24 | 277th | OF Chad Hermansen Pit |
| 25 | 300th | SP Joe Nathan SF |
| 26 | 301st | 3B Kevin Millar Fla |
| 27 | 324th | OF Mark Quinn KC |