| Round | Overall | Player |
|---|---|---|
| 1 | 9th | 1B Todd Helton Col |
| 2 | 16th | 3B Scott Rolen StL |
| 3 | 33rd | SP Ben Sheets Mil |
| 4 | 40th | OF Carl Crawford TB |
| 5 | 57th | SP Jake Peavy SD |
| 6 | 64th | SS Jimmy Rollins Phi |
| 7 | 81st | DH Travis Hafner Cle |
| 8 | 88th | OF Corey Patterson ChN |
| 9 | 105th | RP Jason Isringhausen StL |
| 10 | 112th | SP Odalis Perez LAD |
| 11 | 129th | C Jason Varitek Bos |
| 12 | 136th | OF Juan Pierre Fla |
| 13 | 153rd | 2B Jose Vidro Was |
| 14 | 160th | SP Jaret Wright NYA |
| 15 | 177th | 1B Erubiel Durazo Oak |
| 16 | 184th | OF Matt Holliday Col |
| 17 | 201st | SP Al Leiter NYA |
| 18 | 208th | OF Kevin Mench Tex |
| 19 | 225th | RP Eddie Guardado Sea |
| 20 | 232nd | SP Bronson Arroyo Bos |
| 21 | 249th | OF Cliff Floyd NYN |
| 22 | 256th | 3B Brandon Inge Det |
| 23 | 273rd | 2B Tadahito Iguchi ChA |
| 24 | 280th | SP John Lackey LAA |
| 25 | 297th | SP Gavin Floyd Phi |
| 26 | 304th | RP Shingo Takatsu NYN |
| 27 | 321st | OF Juan Rivera LAA |
| 28 | 328th | SP Brandon Backe Hou |
| 29 | 345th | C Ben Molina LAA |