| Round | Overall | Player |
|---|---|---|
| 1 | 9th | 1B Todd Helton Col |
| 2 | 16th | SS Miguel Tejada Oak |
| 3 | 33rd | OF Adam Dunn Cin |
| 4 | 40th | C Jorge Posada NYA |
| 5 | 57th | OF Carlos Beltran KC |
| 6 | 64th | RP Mariano Rivera NYA |
| 7 | 81st | SP Tom Glavine NYN |
| 8 | 88th | 3B Joe Crede ChA |
| 9 | 105th | 2B Junior Spivey Ari |
| 10 | 112th | RP Jorge Julio Bal |
| 11 | 129th | SP Andy Pettitte NYA |
| 12 | 136th | SP Jamie Moyer Sea |
| 13 | 153rd | C Mike Lieberthal Phi |
| 14 | 160th | 3B Tony Batista Bal |
| 15 | 177th | RP Jose Jimenez Col |
| 16 | 184th | OF Raul Mondesi Ari |
| 17 | 201st | SP Tomo Ohka Mon |
| 18 | 208th | SS Rafael Furcal Atl |
| 19 | 225th | OF Karim Garcia NYA |
| 20 | 232nd | SP Rick Reed Min |
| 21 | 249th | 2B Fernando Vina StL |
| 22 | 256th | OF Carl Everett ChA |
| 23 | 273rd | 1B Scott Spiezio Ana |
| 24 | 280th | SP Mark Redman Fla |
| 25 | 297th | RP Trevor Hoffman SD |
| 26 | 304th | SP Kevin Appier KC |
| 27 | 321st | OF Juan Pierre Fla |
| 28 | 328th | C Miguel Olivo ChA |
| 29 | 345th | SP Jeremy Affeldt KC |