| Round | Overall | Player |
|---|---|---|
| 1 | 4th | 1B Carlos Delgado Tor |
| 2 | 21st | 2B Edgardo Alfonzo NYN |
| 3 | 28th | OF Magglio Ordonez ChA |
| 4 | 45th | SP Bartolo Colon Cle |
| 5 | 52nd | OF Raul Mondesi Tor |
| 6 | 69th | 3B Eric Chavez Oak |
| 7 | 76th | SP Andy Pettitte NYA |
| 8 | 93rd | 1B Richie Sexson Mil |
| 9 | 100th | RP Anthony Alford Fla |
| 10 | 117th | OF J.D. Drew StL |
| 11 | 124th | RP Roberto Hernandez KC |
| 12 | 141st | OF Garret Anderson Ana |
| 13 | 148th | SS Neifi Perez Col |
| 14 | 165th | SP Denny Neagle Col |
| 15 | 172nd | 1B Tony Clark Det |
| 16 | 189th | C Jason Varitek Bos |
| 17 | 196th | SP Shane Reynolds Hou |
| 18 | 213th | SP Jose Lima Hou |
| 19 | 220th | OF Rondell White ChN |
| 20 | 237th | OF Juan Encarnacion Det |
| 21 | 244th | SP Adam Eaton SD |
| 22 | 261st | SP Octavio Dotel Hou |
| 23 | 268th | SP Chris Carpenter Tor |
| 24 | 285th | SP Brad Penny Fla |
| 25 | 292nd | SP C.C. Sabathia Cle |
| 26 | 309th | SS Orlando Cabrera Mon |
| 27 | 316th | SP John Halama Sea |
| 28 | 333rd | OF Daryle Ward Hou |
| 29 | 340th | 3B Pedro Feliz SF |