| Round | Overall | Player |
|---|---|---|
| 1 | 11th | OF Barry Bonds SF |
| 2 | 14th | 2B Bret Boone Sea |
| 3 | 35th | SP Mark Mulder Oak |
| 4 | 38th | C Mike Piazza NYN |
| 5 | 59th | 3B Mike Lowell Fla |
| 6 | 62nd | 1B Mike Sweeney KC |
| 7 | 83rd | SP Mark Buehrle ChA |
| 8 | 86th | OF Juan Gonzalez KC |
| 9 | 107th | OF Reggie Sanders StL |
| 10 | 110th | SP Woody Williams StL |
| 11 | 131st | OF Larry Walker StL |
| 12 | 134th | SP Roger Clemens Hou |
| 13 | 155th | SP Al Leiter NYN |
| 14 | 158th | 3B Jose Valentin ChA |
| 15 | 179th | OF Cliff Floyd NYN |
| 16 | 182nd | RP Matt Mantei Ari |
| 17 | 203rd | RP Billy Koch Fla |
| 18 | 206th | DH Edgar Martinez Sea |
| 19 | 227th | RP Danys Baez TB |
| 20 | 230th | 1B Erubiel Durazo Oak |
| 21 | 251st | OF Jay Payton SD |
| 22 | 254th | SP Tomo Ohka Mon |
| 23 | 275th | 3B Tony Batista Mon |
| 24 | 278th | SS Pokey Reese Bos |
| 25 | 299th | SS Alex Gonzalez Fla |
| 26 | 302nd | SP Chris Carpenter StL |
| 27 | 323rd | C Jason LaRue Cin |
| 28 | 326th | OF Craig Biggio Hou |
| 29 | 347th | SP Brett Tomko SF |