| Round | Overall | Player |
|---|---|---|
| 1 | 12th | 1B Derrek Lee ChN |
| 2 | 13th | SP Johan Santana Min |
| 3 | 36th | 3B Hank Blalock Tex |
| 4 | 37th | 1B Lance Berkman Hou |
| 5 | 60th | SP Rich Harden Oak |
| 6 | 61st | OF Pat Burrell Phi |
| 7 | 84th | SP Josh Beckett Bos |
| 8 | 85th | 2B Rickie Weeks Mil |
| 9 | 108th | SP Cliff Lee Cle |
| 10 | 109th | OF Jose Guillen Was |
| 11 | 132nd | SP Livan Hernandez Ari |
| 12 | 133rd | OF Garret Anderson LAA |
| 13 | 156th | RP Keith Foulke Cle |
| 14 | 157th | SS Carlos Guillen Det |
| 15 | 180th | C Ben Molina SF |
| 16 | 181st | RP Bob Wickman Atl |
| 17 | 204th | SP Shawn Chacon Pit |
| 18 | 205th | 1B Nomar Garciaparra LAD |
| 19 | 228th | 2B Craig Biggio Hou |
| 20 | 229th | SP Kerry Wood ChN |
| 21 | 252nd | C Jason Kendall Oak |
| 22 | 253rd | SS Orlando Cabrera LAA |
| 23 | 276th | DH Frank Thomas Oak |
| 24 | 277th | OF Rocco Baldelli TB |
| 25 | 300th | 3B Joe Randa Pit |
| 26 | 301st | OF Trot Nixon Bos |
| 27 | 324th | SP Bruce Chen Bal |
| 28 | 325th | OF Rondell White Min |
| 29 | 348th | SP Anthony Reyes StL |