| Round | Overall | Player |
|---|---|---|
| 1 | 9th | OF Jason Bay Pit |
| 2 | 16th | OF Bobby Abreu NYA |
| 3 | 33rd | SP Jake Peavy SD |
| 4 | 40th | OF Alfonso Soriano ChA |
| 5 | 57th | 3B Chipper Jones Atl |
| 6 | 64th | SP John Smoltz Atl |
| 7 | 81st | RP Trevor Hoffman SD |
| 8 | 88th | SP Mark Mulder StL |
| 9 | 105th | 1B Jason Giambi NYA |
| 10 | 112th | SP Zach Duke Pit |
| 11 | 129th | 2B Rickie Weeks Mil |
| 12 | 136th | SP Erik Bedard Bal |
| 13 | 153rd | 2B Felipe Lopez Was |
| 14 | 160th | C Kenji Johjima Sea |
| 15 | 177th | C Rod Barajas Tex |
| 16 | 184th | OF Preston Wilson StL |
| 17 | 201st | 1B Nomar Garciaparra LAD |
| 18 | 208th | SP Roger Clemens Hou |
| 19 | 225th | RP Ryan Dempster ChN |
| 20 | 232nd | SP Brad Radke Min |
| 21 | 249th | 3B Pedro Feliz SF |
| 22 | 256th | OF Juan Encarnacion StL |
| 23 | 273rd | RP Chris Ray Bal |
| 24 | 280th | SP Craig Hansen Bos |
| 25 | 297th | 2B Mark Grudzielanek KC |
| 26 | 304th | SP Steve Trachsel NYN |
| 27 | 321st | SS Omar Vizquel SF |
| 28 | 328th | OF Jeromy Burnitz Pit |
| 29 | 345th | SS Anderson Hernandez NYN |