| Round | Overall | Player |
|---|---|---|
| 1 | 11th | OF Barry Bonds SF |
| 2 | 14th | OF Larry Walker Col |
| 3 | 35th | SP Greg Maddux Atl |
| 4 | 38th | 1B Jason Giambi Oak |
| 5 | 59th | 3B Robin Ventura NYN |
| 6 | 62nd | RP Robb Nen SF |
| 7 | 83rd | RP Roberto Hernandez TB |
| 8 | 86th | RP John Rocker Atl |
| 9 | 107th | SP Al Leiter NYN |
| 10 | 110th | 1B Kevin Young Pit |
| 11 | 131st | C Darrin Fletcher Tor |
| 12 | 134th | OF Luis Gonzalez Ari |
| 13 | 155th | 2B Damion Easley Det |
| 14 | 158th | SP Jamie Moyer Sea |
| 15 | 179th | OF Rusty Greer Tex |
| 16 | 182nd | OF Ellis Burks SF |
| 17 | 203rd | 3B Joe Randa KC |
| 18 | 206th | SP Todd Stottlemyre Ari |
| 19 | 227th | SP Scott Erickson Bal |
| 20 | 230th | SP Dave Burba Cle |
| 21 | 251st | C Ben Petrick Col |
| 22 | 254th | SP Roy Halladay Tor |
| 23 | 275th | SP John Halama Sea |
| 24 | 278th | SP Jaret Wright Cle |
| 25 | 299th | SS Alex Gonzalez Tor |
| 26 | 302nd | 1B Brian Daubach Bos |
| 27 | 323rd | SP Chris Brock Phi |