| Round | Overall | Player |
|---|---|---|
| 1 | 12th | 3B Chipper Jones Atl |
| 2 | 13th | SP Pedro Martinez Bos |
| 3 | 36th | OF Raul Mondesi Tor |
| 4 | 37th | RP Billy Wagner Hou |
| 5 | 60th | OF Carlos Beltran KC |
| 6 | 61st | 1B Sean Casey Cin |
| 7 | 84th | OF Ray Lankford StL |
| 8 | 85th | SS Edgar Renteria StL |
| 9 | 108th | OF Dante Bichette Cin |
| 10 | 109th | C Jason Varitek Bos |
| 11 | 132nd | SP Omar Daal Ari |
| 12 | 133rd | SP Justin Thompson Tex |
| 13 | 156th | SP Dustin Hermanson Mon |
| 14 | 157th | SP Kevin Appier Oak |
| 15 | 180th | 2B Homer Bush Tor |
| 16 | 181st | OF Geoff Jenkins Mil |
| 17 | 204th | OF Doug Glanville Phi |
| 18 | 205th | SP Kent Bottenfield Ana |
| 19 | 228th | OF Darin Erstad Ana |
| 20 | 229th | 1B Rico Brogna Phi |
| 21 | 252nd | 2B Pokey Reese Cin |
| 22 | 253rd | C Brad Ausmus Det |
| 23 | 276th | 2B Todd Walker Min |
| 24 | 277th | DH Jeremy Giambi Oak |
| 25 | 300th | 3B Scott Brosius NYA |
| 26 | 301st | RP Orber Moreno KC |
| 27 | 324th | OF Mark Quinn KC |