| Round | Overall | Player |
|---|---|---|
| 1 | 5th | SS Nomar Garciaparra Bos |
| 2 | 20th | OF Chipper Jones Atl |
| 3 | 29th | RP Mariano Rivera NYA |
| 4 | 44th | C Paul Lo Duca LA |
| 5 | 53rd | 1B Phil Nevin SD |
| 6 | 68th | SP Mark Buehrle ChA |
| 7 | 77th | OF Ryan Klesko SD |
| 8 | 92nd | SP Bartolo Colon Cle |
| 9 | 101st | OF Carlos Beltran KC |
| 10 | 116th | SP C.C. Sabathia Cle |
| 11 | 125th | 3B Sean Burroughs SD |
| 12 | 140th | 3B Jeff Cirillo Sea |
| 13 | 149th | SP A.J. Burnett Fla |
| 14 | 164th | SS Rafael Furcal Atl |
| 15 | 173rd | 1B Tony Clark Bos |
| 16 | 188th | SP Ramon Ortiz Ana |
| 17 | 197th | DH Nick Johnson NYA |
| 18 | 212th | OF Frank Catalanotto Tex |
| 19 | 221st | RP Braden Looper Fla |
| 20 | 236th | OF Corey Patterson ChN |
| 21 | 245th | SP Jason Bere ChN |
| 22 | 260th | SP Brian Lawrence SD |
| 23 | 269th | C Gary Bennett Col |
| 24 | 284th | DH David Ortiz Min |
| 25 | 293rd | OF Vernon Wells Tor |
| 26 | 308th | 2B Ron Belliard Mil |
| 27 | 317th | SP Kurt Ainsworth SF |
| 28 | 332nd | SP Jorge Julio Bal |
| 29 | 341st | 2B Homer Bush Tor |