| Round | Overall | Player |
|---|---|---|
| 1 | 11th | 1B Jeff Bagwell Hou |
| 2 | 14th | OF Shawn Green LA |
| 3 | 35th | OF Gary Sheffield Atl |
| 4 | 38th | RP Robb Nen SF |
| 5 | 59th | SP Kevin Brown LA |
| 6 | 62nd | SP Javier Vazquez Mon |
| 7 | 83rd | OF Carlos Beltran KC |
| 8 | 86th | RP John Smoltz Atl |
| 9 | 107th | SP Eric Milton Min |
| 10 | 110th | 3B Edgardo Alfonzo NYN |
| 11 | 131st | C Javy Lopez Atl |
| 12 | 134th | OF Juan Pierre Col |
| 13 | 155th | RP Jose Mesa Phi |
| 14 | 158th | SP Aaron Sele Ana |
| 15 | 179th | OF Carlos Lee ChA |
| 16 | 182nd | 1B Derrek Lee Fla |
| 17 | 203rd | OF Reggie Sanders SF |
| 18 | 206th | SP Roy Halladay Tor |
| 19 | 227th | SP Scott Erickson Bal |
| 20 | 230th | DH Brad Fullmer Ana |
| 21 | 251st | SP Andy Ashby LA |
| 22 | 254th | OF Ben Grieve TB |
| 23 | 275th | SP Jason Bere ChN |
| 24 | 278th | SS Mike Bordick Bal |
| 25 | 299th | 3B Travis Fryman Cle |
| 26 | 302nd | SS Felipe Lopez Tor |
| 27 | 323rd | 2B Carlos Febles KC |
| 28 | 326th | C Brad Ausmus Hou |
| 29 | 347th | SP Jeff Suppan KC |