| Round | Overall | Player |
|---|---|---|
| 1 | 10th | SP Johan Santana Min |
| 2 | 15th | 1B Mark Teixeira Tex |
| 3 | 34th | SS Derek Jeter NYA |
| 4 | 39th | OF Hideki Matsui NYA |
| 5 | 58th | SP Pedro Martinez NYN |
| 6 | 63rd | OF Carlos Lee Mil |
| 7 | 82nd | OF Johnny Damon Bos |
| 8 | 87th | C Javy Lopez Bal |
| 9 | 106th | SP John Thomson Atl |
| 10 | 111th | RP Octavio Dotel Oak |
| 11 | 130th | OF Brad Wilkerson Was |
| 12 | 135th | SP Kelvim Escobar LAA |
| 13 | 154th | 2B Ray Durham SF |
| 14 | 159th | SS Orlando Cabrera LAA |
| 15 | 178th | SP Adam Eaton SD |
| 16 | 183rd | C Ramon Hernandez SD |
| 17 | 202nd | 3B Bill Mueller Bos |
| 18 | 207th | SP Dan Haren Oak |
| 19 | 226th | SP Paul Byrd LAA |
| 20 | 231st | OF Mike Cameron NYN |
| 21 | 250th | 1B Scott Hatteberg Oak |
| 22 | 255th | 3B Ty Wigginton Pit |
| 23 | 274th | 2B Aaron Miles Col |
| 24 | 279th | OF Mark Kotsay Oak |
| 25 | 298th | RP Danys Baez TB |
| 26 | 303rd | SP Tim Wakefield Bos |
| 27 | 322nd | SP Shawn Estes Ari |
| 28 | 327th | RP Tom Gordon NYA |
| 29 | 346th | RP Chad Cordero Was |