| Round | Overall | Player |
|---|---|---|
| 1 | 1st | SS Alex Rodriguez Tex |
| 2 | 24th | RP Mariano Rivera NYA |
| 3 | 25th | OF Lance Berkman Hou |
| 4 | 48th | 3B Eric Chavez Oak |
| 5 | 49th | SP Kevin Brown LA |
| 6 | 72nd | OF Ryan Klesko SD |
| 7 | 73rd | RP John Smoltz Atl |
| 8 | 96th | SP Wade Miller Hou |
| 9 | 97th | 1B Sean Casey Cin |
| 10 | 120th | OF Jeromy Burnitz NYN |
| 11 | 121st | 2B Ray Durham ChA |
| 12 | 144th | SP C.C. Sabathia Cle |
| 13 | 145th | SP Cory Lidle Oak |
| 14 | 168th | C Charles Johnson Fla |
| 15 | 169th | 3B Sean Burroughs SD |
| 16 | 192nd | SP Mike Hampton Col |
| 17 | 193rd | OF Brian Jordan LA |
| 18 | 216th | 1B Carlos Pena Oak |
| 19 | 217th | DH Nick Johnson NYA |
| 20 | 240th | SP Chris Carpenter Tor |
| 21 | 241st | RP Scott Strickland Mon |
| 22 | 264th | OF Gabe Kapler Tex |
| 23 | 265th | SP Brian Lawrence SD |
| 24 | 288th | SP Rick Helling Ari |
| 25 | 289th | C Ben Davis Sea |
| 26 | 312th | OF Ben Grieve TB |
| 27 | 313th | RP Vicente Padilla Phi |
| 28 | 336th | SS Neifi Perez KC |
| 29 | 337th | 2B Ron Belliard Mil |