| Round | Overall | Player |
|---|---|---|
| 1 | 2nd | OF Vladimir Guerrero LAA |
| 2 | 23rd | SS Derek Jeter NYA |
| 3 | 26th | 1B Carlos Delgado NYN |
| 4 | 47th | 1B Lance Berkman Hou |
| 5 | 50th | 3B Hank Blalock Tex |
| 6 | 71st | RP Francisco Rodriguez LAA |
| 7 | 74th | C Jason Varitek Bos |
| 8 | 95th | 2B Brian Roberts Bal |
| 9 | 98th | SP Josh Beckett Bos |
| 10 | 119th | SP Livan Hernandez Ari |
| 11 | 122nd | RP Eric Gagne LAD |
| 12 | 143rd | OF Magglio Ordonez Det |
| 13 | 146th | OF Jose Guillen Was |
| 14 | 167th | SP Jake Westbrook Cle |
| 15 | 170th | SP Tom Glavine NYN |
| 16 | 191st | RP Todd Jones Det |
| 17 | 194th | OF David Dellucci Cle |
| 18 | 215th | SP Jarrod Washburn Sea |
| 19 | 218th | SP Rodrigo Lopez Col |
| 20 | 239th | 3B Ryan Zimmerman Was |
| 21 | 242nd | SP Greg Maddux SD |
| 22 | 263rd | 2B Josh Barfield Cle |
| 23 | 266th | SP Carl Pavano NYA |
| 24 | 287th | OF Brad Hawpe Col |
| 25 | 290th | 1B Phil Nevin Min |
| 26 | 311th | C Johnny Estrada Mil |
| 27 | 314th | SS Hanley Ramirez Fla |
| 28 | 335th | OF Jason Michaels Cle |
| 29 | 338th | SP Orlando Hernandez NYN |