| Round | Overall | Player |
|---|---|---|
| 1 | 6th | OF Alfonso Soriano ChN |
| 2 | 19th | OF Jason Bay Pit |
| 3 | 30th | SP Roy Oswalt Hou |
| 4 | 43rd | SS Hanley Ramirez Fla |
| 5 | 54th | OF Nick Swisher ChA |
| 6 | 67th | 1B Adrian Gonzalez SD |
| 7 | 78th | 3B Eric Chavez Oak |
| 8 | 91st | OF J.D. Drew Bos |
| 9 | 102nd | SP Chris Capuano Mil |
| 10 | 115th | SP Erik Bedard Bal |
| 11 | 126th | 3B Alex Gordon KC |
| 12 | 139th | SS Felipe Lopez Was |
| 13 | 150th | SP Jake Westbrook Cle |
| 14 | 163rd | SP Anibal Sanchez Fla |
| 15 | 174th | SP Dave Bush Mil |
| 16 | 187th | C Chris Iannetta Col |
| 17 | 198th | SP Jeremy Sowers Cle |
| 18 | 211th | SP Nate Robertson Det |
| 19 | 222nd | SP Livan Hernandez Ari |
| 20 | 235th | 1B Nick Johnson Was |
| 21 | 246th | 2B Marcus Giles SD |
| 22 | 259th | 1B Rich Aurilia SF |
| 23 | 270th | C Mike Napoli LAA |
| 24 | 283rd | SP Oliver Perez NYN |
| 25 | 294th | SS Jason Bartlett Min |
| 26 | 307th | SP Adam Loewen Bal |
| 27 | 318th | OF Jose Guillen KC |
| 28 | 331st | SP Paul Maholm Pit |
| 29 | 342nd | OF Brad Wilkerson Tex |