| Round | Overall | Player |
|---|---|---|
| 1 | 9th | 1B Jim Thome Phi |
| 2 | 16th | RP Eric Gagne LA |
| 3 | 33rd | OF Lance Berkman Hou |
| 4 | 40th | SP Mark Mulder Oak |
| 5 | 57th | 3B Troy Glaus Ana |
| 6 | 64th | SP Kevin Brown NYA |
| 7 | 81st | OF Jim Edmonds StL |
| 8 | 88th | 2B Ray Durham SF |
| 9 | 105th | C Jason Varitek Bos |
| 10 | 112th | OF Ryan Klesko SD |
| 11 | 129th | SP Jamie Moyer Sea |
| 12 | 136th | RP Francisco Cordero Tex |
| 13 | 153rd | 1B Josh Phelps Cle |
| 14 | 160th | 3B Joe Crede ChA |
| 15 | 177th | SP Kip Wells Pit |
| 16 | 184th | OF Jermaine Dye Oak |
| 17 | 201st | OF Milton Bradley LA |
| 18 | 208th | 1B Jason Phillips NYN |
| 19 | 225th | SP Steve Trachsel NYN |
| 20 | 232nd | SS Cristian Guzman Min |
| 21 | 249th | RP Danny Graves Cin |
| 22 | 256th | 2B Junior Spivey Mil |
| 23 | 273rd | SP Ted Lilly Tor |
| 24 | 280th | SS Carlos Guillen Det |
| 25 | 297th | SP Zach Day Mon |
| 26 | 304th | 1B Carlos Pena Det |
| 27 | 321st | SP Chris Carpenter StL |
| 28 | 328th | RP David Riske Cle |
| 29 | 345th | C Robby Hammock Ari |