| Round | Overall | Player |
|---|---|---|
| 1 | 12th | 1B Jason Giambi NYA |
| 2 | 13th | SS Derek Jeter NYA |
| 3 | 36th | OF Bobby Abreu Phi |
| 4 | 37th | SP Bartolo Colon ChA |
| 5 | 60th | RP Robb Nen SF |
| 6 | 61st | SP Odalis Perez LA |
| 7 | 84th | OF Torii Hunter Min |
| 8 | 85th | 2B Ray Durham SF |
| 9 | 108th | RP Mike Williams Phi |
| 10 | 109th | DH Erubiel Durazo Oak |
| 11 | 132nd | 3B Jose Hernandez Pit |
| 12 | 133rd | SP Al Leiter NYN |
| 13 | 156th | OF Randy Winn Sea |
| 14 | 157th | 3B Mark Bellhorn Col |
| 15 | 180th | SP Rodrigo Lopez Bal |
| 16 | 181st | OF Steve Finley Ari |
| 17 | 204th | C Einar Diaz Tex |
| 18 | 205th | SP Elmer Dessens Ari |
| 19 | 228th | SP Jason Simontacchi StL |
| 20 | 229th | 3B Robin Ventura LA |
| 21 | 252nd | SP Kenny Rogers Min |
| 22 | 253rd | OF Kenny Lofton ChN |
| 23 | 276th | SP Steve Trachsel NYN |
| 24 | 277th | OF Marlon Byrd Phi |
| 25 | 300th | SP Jake Peavy SD |
| 26 | 301st | 1B David Ortiz Bos |
| 27 | 324th | 2B Jerry Hairston Jr. Bal |
| 28 | 325th | C Brandon Inge Det |
| 29 | 348th | OF Matt Lawton Cle |