| Round | Overall | Player |
|---|---|---|
| 1 | 1st | 3B Alex Rodriguez NYA |
| 2 | 24th | 1B Todd Helton Col |
| 3 | 25th | OF Carlos Beltran NYN |
| 4 | 48th | 2B Jorge Cantu TB |
| 5 | 49th | SP Randy Johnson NYA |
| 6 | 72nd | OF Vernon Wells Tor |
| 7 | 73rd | RP Eric Gagne LAD |
| 8 | 96th | SP Barry Zito Oak |
| 9 | 97th | RP Todd Jones Det |
| 10 | 120th | OF Magglio Ordonez Det |
| 11 | 121st | SS Bobby Crosby Oak |
| 12 | 144th | C Kenji Johjima Sea |
| 13 | 145th | SP John Patterson Was |
| 14 | 168th | SP Matt Morris SF |
| 15 | 169th | SP Tom Glavine NYN |
| 16 | 192nd | OF Shawn Green NYN |
| 17 | 193rd | OF Luis Gonzalez Ari |
| 18 | 216th | SP Greg Maddux SD |
| 19 | 217th | C Mike Lieberthal Phi |
| 20 | 240th | 1B Ben Broussard Sea |
| 21 | 241st | SS Juan Uribe ChA |
| 22 | 264th | 3B Tony Batista Min |
| 23 | 265th | RP Danys Baez Bal |
| 24 | 288th | 2B Todd Walker SD |
| 25 | 289th | SP Russ Ortiz Bal |
| 26 | 312th | SP Horacio Ramirez Atl |
| 27 | 313th | SP Jamie Moyer Phi |
| 28 | 336th | SP Craig Hansen Bos |
| 29 | 337th | OF Corey Patterson Bal |