| Round | Overall | Player |
|---|---|---|
| 1 | 12th | OF Sammy Sosa ChN |
| 2 | 13th | OF Gary Sheffield NYA |
| 3 | 36th | C Javy Lopez Bal |
| 4 | 37th | 1B Derrek Lee ChN |
| 5 | 60th | SP Josh Beckett Fla |
| 6 | 61st | SP Kevin Brown NYA |
| 7 | 84th | SP Johan Santana Min |
| 8 | 85th | OF Luis Gonzalez Ari |
| 9 | 108th | RP Arthur Rhodes Oak |
| 10 | 109th | RP Armando Benitez Fla |
| 11 | 132nd | OF Ryan Klesko SD |
| 12 | 133rd | 3B Bill Mueller Bos |
| 13 | 156th | SP Brad Penny LA |
| 14 | 157th | SS Bobby Crosby Oak |
| 15 | 180th | SP Kelvim Escobar Ana |
| 16 | 181st | 2B Luis Castillo Fla |
| 17 | 204th | C Joe Mauer Min |
| 18 | 205th | OF Trot Nixon Bos |
| 19 | 228th | SP Ramon Ortiz Ana |
| 20 | 229th | SP A.J. Burnett Fla |
| 21 | 252nd | 1B Carlos Pena Det |
| 22 | 253rd | 1B Jason Phillips NYN |
| 23 | 276th | OF Jerry Hairston Jr. Bal |
| 24 | 277th | 3B Alex Gonzalez TB |
| 25 | 300th | SP Kirk Rueter SF |
| 26 | 301st | OF Steve Finley LA |
| 27 | 324th | 3B Brandon Larson Cin |
| 28 | 325th | SP Claudio Vargas Mon |
| 29 | 348th | SS Enrique Wilson NYA |