| Round | Overall | Player |
|---|---|---|
| 1 | 6th | OF Sammy Sosa ChN |
| 2 | 19th | SS Miguel Tejada Oak |
| 3 | 30th | 3B Scott Rolen StL |
| 4 | 43rd | SP Mark Mulder Oak |
| 5 | 54th | SP Mike Mussina NYA |
| 6 | 67th | OF Bernie Williams NYA |
| 7 | 78th | SP Odalis Perez LA |
| 8 | 91st | 2B Roberto Alomar ChA |
| 9 | 102nd | SP A.J. Burnett Fla |
| 10 | 115th | SP Ramon Ortiz Ana |
| 11 | 126th | 1B Mo Vaughn NYN |
| 12 | 139th | OF Carlos Lee ChA |
| 13 | 150th | 3B Hank Blalock Tex |
| 14 | 163rd | OF Jose Cruz Jr SF |
| 15 | 174th | SP Brian Lawrence SD |
| 16 | 187th | SP Brad Penny Fla |
| 17 | 198th | 1B Tino Martinez StL |
| 18 | 211th | OF Juan Encarnacion Fla |
| 19 | 222nd | SP Ryan Dempster Cin |
| 20 | 235th | C Jason LaRue Cin |
| 21 | 246th | SP Adam Eaton SD |
| 22 | 259th | SS Carlos Guillen Sea |
| 23 | 270th | 2B Ron Belliard Col |
| 24 | 283rd | OF Kevin Millar Bos |
| 25 | 294th | C Josh Bard Cle |
| 26 | 307th | SP Casey Fossum Bos |
| 27 | 318th | 3B Dean Palmer Det |
| 28 | 331st | OF Michael Cuddyer Min |
| 29 | 342nd | SP Jeremy Affeldt KC |