| Round | Overall | Player |
|---|---|---|
| 1 | 12th | SP Johan Santana Min |
| 2 | 13th | SS Mike Young Tex |
| 3 | 36th | SP Roy Oswalt Hou |
| 4 | 37th | 1B Paul Konerko ChA |
| 5 | 60th | RP Joe Nathan Min |
| 6 | 61st | 2B Marcus Giles Atl |
| 7 | 84th | C Joe Mauer Min |
| 8 | 85th | 3B Troy Glaus Tor |
| 9 | 108th | OF Cliff Floyd ChA |
| 10 | 109th | SP Jon Garland ChA |
| 11 | 132nd | 3B Chone Figgins LAA |
| 12 | 133rd | SP Chris Capuano Mil |
| 13 | 156th | OF Luis Gonzalez Ari |
| 14 | 157th | 1B Mike Jacobs Fla |
| 15 | 180th | SP Jarrod Washburn Sea |
| 16 | 181st | OF Jason Lane Hou |
| 17 | 204th | 2B Craig Biggio Hou |
| 18 | 205th | SS Khalil Greene SD |
| 19 | 228th | 3B Mike Lowell Bos |
| 20 | 229th | SP Jason Marquis ChA |
| 21 | 252nd | OF David Dellucci Cle |
| 22 | 253rd | 3B Edwin Encarnacion Cin |
| 23 | 276th | C Brian McCann Atl |
| 24 | 277th | RP Danys Baez Bal |
| 25 | 300th | SP Aaron Cook Col |
| 26 | 301st | SP Kyle Lohse Cin |
| 27 | 324th | RP Chad Orvella TB |
| 28 | 325th | 2B Ian Kinsler Tex |
| 29 | 348th | OF Emil Brown KC |