| Round | Overall | Player |
|---|---|---|
| 1 | 7th | 1B Jason Giambi NYA |
| 2 | 18th | OF Chipper Jones Atl |
| 3 | 31st | SP Tim Hudson Oak |
| 4 | 42nd | 1B Phil Nevin SD |
| 5 | 55th | RP Trevor Hoffman SD |
| 6 | 66th | C Jason Kendall Pit |
| 7 | 79th | 2B Craig Biggio Hou |
| 8 | 90th | SP Mark Buehrle ChA |
| 9 | 103rd | SS Cristian Guzman Min |
| 10 | 114th | OF Raul Mondesi Tor |
| 11 | 127th | OF Preston Wilson Fla |
| 12 | 138th | SP A.J. Burnett Fla |
| 13 | 151st | OF Jeff Conine Bal |
| 14 | 162nd | SP Jarrod Washburn Ana |
| 15 | 175th | 3B Sean Burroughs SD |
| 16 | 186th | 1B Doug Mientkiewicz Min |
| 17 | 199th | 2B Jose Offerman Bos |
| 18 | 210th | RP Mike Williams Pit |
| 19 | 223rd | SP Rick Reed Min |
| 20 | 234th | SP Steve Sparks Det |
| 21 | 247th | SS Neifi Perez KC |
| 22 | 258th | SP James Baldwin Sea |
| 23 | 271st | C Michael Barrett Mon |
| 24 | 282nd | OF Mark Kotsay SD |
| 25 | 295th | DH Brad Fullmer Ana |
| 26 | 306th | OF Rusty Greer Tex |
| 27 | 319th | 3B Joe Randa KC |
| 28 | 330th | SP Bobby J. Jones SD |
| 29 | 343rd | SP Rick Ankiel StL |