| Round | Overall | Player |
|---|---|---|
| 1 | 12th | OF Carlos Beltran Hou |
| 2 | 13th | 1B Jim Thome Phi |
| 3 | 36th | 3B Eric Chavez Oak |
| 4 | 37th | SP Mark Prior ChN |
| 5 | 60th | OF Andruw Jones Atl |
| 6 | 61st | RP Eddie Guardado Sea |
| 7 | 84th | C Jason Varitek Bos |
| 8 | 85th | SP Dontrelle Willis Fla |
| 9 | 108th | OF Richard Hidalgo NYN |
| 10 | 109th | SP Jamie Moyer Sea |
| 11 | 132nd | SS Jose Reyes NYN |
| 12 | 133rd | SS Alex Cintron Ari |
| 13 | 156th | OF Jody Gerut Cle |
| 14 | 157th | SP Al Leiter NYN |
| 15 | 180th | SP Byung-Hyun Kim Bos |
| 16 | 181st | 3B Casey Blake Cle |
| 17 | 204th | SP Steve Trachsel NYN |
| 18 | 205th | 2B Eric Young Tex |
| 19 | 228th | RP Shigetoshi Hasegawa Sea |
| 20 | 229th | RP Tim Worrell Phi |
| 21 | 252nd | 1B Jason Phillips NYN |
| 22 | 253rd | OF Mike Cameron NYN |
| 23 | 276th | SP Tony Armas Jr. Mon |
| 24 | 277th | SP Darren Oliver Hou |
| 25 | 300th | 1B Carlos Pena Det |
| 26 | 301st | 2B Keith Ginter Mil |
| 27 | 324th | SS Jack Wilson Pit |
| 28 | 325th | SP Shane Reynolds Ari |
| 29 | 348th | SP Brandon Claussen Cin |