| Round | Overall | Player |
|---|---|---|
| 1 | 11th | SP Johan Santana Min |
| 2 | 14th | SS Miguel Tejada Bal |
| 3 | 35th | SP Chris Carpenter StL |
| 4 | 38th | 1B Paul Konerko ChA |
| 5 | 59th | SP Pedro Martinez NYN |
| 6 | 62nd | RP Eric Gagne LAD |
| 7 | 83rd | 3B Scott Rolen StL |
| 8 | 86th | OF Johnny Damon NYA |
| 9 | 107th | OF Brian S. Giles SD |
| 10 | 110th | RP Francisco Cordero Mil |
| 11 | 131st | 2B Robinson Cano NYA |
| 12 | 134th | SP A.J. Burnett Tor |
| 13 | 155th | C Jorge Posada NYA |
| 14 | 158th | RP Bob Wickman Atl |
| 15 | 179th | OF Jermaine Dye ChA |
| 16 | 182nd | SP Matt Cain SF |
| 17 | 203rd | 1B Dan Johnson Oak |
| 18 | 206th | OF Curtis Granderson Det |
| 19 | 227th | C Jason Kendall Oak |
| 20 | 230th | 2B Josh Barfield Cle |
| 21 | 251st | OF Randy Winn SF |
| 22 | 254th | SP Shawn Chacon Pit |
| 23 | 275th | SS Hanley Ramirez Fla |
| 24 | 278th | SP Jon Papelbon Bos |
| 25 | 299th | 3B Joe Crede ChA |
| 26 | 302nd | SP Carl Pavano NYA |
| 27 | 323rd | RP Yhency Brazoban LAD |
| 28 | 326th | OF Shannon Stewart Min |
| 29 | 347th | OF Lastings Milledge NYN |