| Round | Overall | Player |
|---|---|---|
| 1 | 1st | 3B Alex Rodriguez NYA |
| 2 | 24th | 2B Bret Boone Sea |
| 3 | 25th | SP Pedro Martinez Bos |
| 4 | 48th | SP Randy Johnson Ari |
| 5 | 49th | 1B Jeff Bagwell Hou |
| 6 | 72nd | SP Johan Santana Min |
| 7 | 73rd | OF Andruw Jones Atl |
| 8 | 96th | C Jason Varitek Bos |
| 9 | 97th | RP Jason Isringhausen StL |
| 10 | 120th | RP Armando Benitez Fla |
| 11 | 121st | SS Bobby Crosby Oak |
| 12 | 144th | OF Jose Guillen Ana |
| 13 | 145th | OF Bernie Williams NYA |
| 14 | 168th | 1B Kevin Millar Bos |
| 15 | 169th | RP Joe Nathan Min |
| 16 | 192nd | SP Mike Hampton Atl |
| 17 | 193rd | OF Dmitri Young Det |
| 18 | 216th | SP Kelvim Escobar Ana |
| 19 | 217th | 3B Joe Crede ChA |
| 20 | 240th | SS Alex Gonzalez Fla |
| 21 | 241st | SP Ramon Ortiz Ana |
| 22 | 264th | OF Moises Alou ChN |
| 23 | 265th | OF Steve Finley LA |
| 24 | 288th | SP Tim Wakefield Bos |
| 25 | 289th | SP Byung-Hyun Kim Bos |
| 26 | 312th | C Greg Myers Tor |
| 27 | 313th | 2B Orlando Hudson Tor |
| 28 | 336th | OF Luis Matos Bal |
| 29 | 337th | 1B Carlos Pena Det |