| Round | Overall | Player |
|---|---|---|
| 1 | 9th | SP Johan Santana Min |
| 2 | 16th | SP Randy Johnson NYA |
| 3 | 33rd | OF Barry Bonds SF |
| 4 | 40th | SP Pedro Martinez NYN |
| 5 | 57th | OF Vernon Wells Tor |
| 6 | 64th | SP Jake Peavy SD |
| 7 | 81st | 3B Mike Lowell Fla |
| 8 | 88th | SP John Smoltz Atl |
| 9 | 105th | SP A.J. Burnett Fla |
| 10 | 112th | 1B Phil Nevin Tex |
| 11 | 129th | SS Jose Reyes NYN |
| 12 | 136th | SP Jake Westbrook Cle |
| 13 | 153rd | SP Andy Pettitte Hou |
| 14 | 160th | C Mike Lieberthal Phi |
| 15 | 177th | OF Matt Holliday Col |
| 16 | 184th | DH Frank Thomas ChA |
| 17 | 201st | 3B Chone Figgins LAA |
| 18 | 208th | OF Jermaine Dye ChA |
| 19 | 225th | SP Gil Meche Sea |
| 20 | 232nd | SP Jason Marquis StL |
| 21 | 249th | 3B Bill Mueller Bos |
| 22 | 256th | SP Kazuhisa Ishii NYN |
| 23 | 273rd | C Toby Hall TB |
| 24 | 280th | SS Julio Lugo TB |
| 25 | 297th | 3B Michael Cuddyer Min |
| 26 | 304th | 1B Nick Johnson Was |
| 27 | 321st | 2B Luis Castillo Fla |
| 28 | 328th | SP Cory Lidle Phi |
| 29 | 345th | OF Carl Everett ChA |