| Round | Overall | Player |
|---|---|---|
| 1 | 4th | 1B Derrek Lee ChN |
| 2 | 21st | OF Andruw Jones Atl |
| 3 | 28th | 3B Aramis Ramirez ChN |
| 4 | 45th | SP Chris Carpenter StL |
| 5 | 52nd | OF Barry Bonds SF |
| 6 | 69th | SP Rich Harden Oak |
| 7 | 76th | 2B Rickie Weeks Mil |
| 8 | 93rd | 3B Chone Figgins LAA |
| 9 | 100th | SS Clint Barmes Col |
| 10 | 117th | RP Jose Valverde Ari |
| 11 | 124th | SP Freddy Garcia ChA |
| 12 | 141st | SP Jose Contreras ChA |
| 13 | 148th | RP Ryan Dempster ChN |
| 14 | 165th | SP Kerry Wood ChN |
| 15 | 172nd | OF Jason Lane Hou |
| 16 | 189th | SP Kelvim Escobar LAA |
| 17 | 196th | OF Moises Alou SF |
| 18 | 213th | 1B Nick Johnson Was |
| 19 | 220th | SP Carlos Silva Min |
| 20 | 237th | C Rod Barajas Tex |
| 21 | 244th | SP Shawn Chacon Pit |
| 22 | 261st | SP Jorge Sosa StL |
| 23 | 268th | 2B Luis A. Gonzalez Col |
| 24 | 285th | C Jason LaRue KC |
| 25 | 292nd | OF Brady Clark Mil |
| 26 | 309th | 3B Brandon Inge Det |
| 27 | 316th | OF Reggie Sanders KC |
| 28 | 333rd | SP Brandon McCarthy Tex |