| Round | Overall | Player |
|---|---|---|
| 1 | 2nd | 1B Todd Helton Col |
| 2 | 23rd | OF Bobby Abreu Phi |
| 3 | 26th | SP Mike Mussina NYA |
| 4 | 47th | C Jorge Posada NYA |
| 5 | 50th | SS Rich Aurilia SF |
| 6 | 71st | OF Ryan Klesko SD |
| 7 | 74th | 2B Ray Durham ChA |
| 8 | 95th | RP Jason Isringhausen StL |
| 9 | 98th | DH Edgar Martinez Sea |
| 10 | 119th | SP Brad Radke Min |
| 11 | 122nd | 3B Jeff Cirillo Sea |
| 12 | 143rd | OF Geoff Jenkins Mil |
| 13 | 146th | RP Byung-Hyun Kim Ari |
| 14 | 167th | SP Robert Person Phi |
| 15 | 170th | SP Randy Wolf Phi |
| 16 | 191st | SP Shawn Estes NYN |
| 17 | 194th | RP Scott Strickland Mon |
| 18 | 215th | SP Steve Sparks Det |
| 19 | 218th | OF Reggie Sanders SF |
| 20 | 239th | RP Eddie Guardado Min |
| 21 | 242nd | OF Frank Catalanotto Tex |
| 22 | 263rd | OF Roger Cedeno NYN |
| 23 | 266th | SS Jose Hernandez Mil |
| 24 | 287th | SP Steve Trachsel NYN |
| 25 | 290th | 1B Kevin Young Pit |
| 26 | 311th | SP Brian Anderson Ari |
| 27 | 314th | C A.J. Pierzynski Min |
| 28 | 335th | 2B Mark Grudzielanek LA |
| 29 | 338th | 3B Shane Halter Det |