| Round | Overall | Player |
|---|---|---|
| 1 | 12th | 1B Carlos Delgado Tor |
| 2 | 13th | OF Barry Bonds SF |
| 3 | 36th | SP Tim Hudson Oak |
| 4 | 37th | OF Magglio Ordonez ChA |
| 5 | 60th | 3B Tony Batista Tor |
| 6 | 61st | SP Roger Clemens NYA |
| 7 | 84th | 1B Ryan Klesko SD |
| 8 | 85th | SP Kerry Wood ChN |
| 9 | 108th | RP Bob Wickman Cle |
| 10 | 109th | 2B Todd Walker Col |
| 11 | 132nd | OF Steve Finley Ari |
| 12 | 133rd | SS Neifi Perez Col |
| 13 | 156th | OF Todd Hollandsworth Col |
| 14 | 157th | C Ben Molina Ana |
| 15 | 180th | 3B Mike Lowell Fla |
| 16 | 181st | SP Glendon Rusch NYN |
| 17 | 204th | SP Scott Williamson Cin |
| 18 | 205th | SP Adam Eaton SD |
| 19 | 228th | SP Ryan Kohlmeier Bal |
| 20 | 229th | OF Derek Bell Pit |
| 21 | 252nd | SS Deivi Cruz Det |
| 22 | 253rd | C Ramon Hernandez Oak |
| 23 | 276th | 2B Bret Boone Sea |
| 24 | 277th | SP Jarrod Washburn Ana |
| 25 | 300th | OF Mark Kotsay SD |
| 26 | 301st | OF Travis Lee Phi |
| 27 | 324th | OF Eric Owens Fla |
| 28 | 325th | OF Tony Gwynn SD |
| 29 | 348th | RP Jeff Brantley Tex |