| Round | Overall | Player |
|---|---|---|
| 1 | 4th | 1B Ryan Howard Phi |
| 2 | 21st | OF Manny Ramirez Bos |
| 3 | 28th | 1B Justin Morneau Min |
| 4 | 45th | RP Mariano Rivera NYA |
| 5 | 52nd | SP Jon Papelbon Bos |
| 6 | 69th | SP John Lackey LAA |
| 7 | 76th | 1B Jason Giambi NYA |
| 8 | 93rd | 2B Rickie Weeks Mil |
| 9 | 100th | 3B Chipper Jones Atl |
| 10 | 117th | SP Cole Hamels Phi |
| 11 | 124th | 2B Dan Uggla Fla |
| 12 | 141st | SP Jered Weaver LAA |
| 13 | 148th | SP Adam Wainwright StL |
| 14 | 165th | SP John Patterson Was |
| 15 | 172nd | SP Chien-Ming Wang NYA |
| 16 | 189th | SP Kei Igawa NYA |
| 17 | 196th | 3B Joe Crede ChA |
| 18 | 213th | OF Josh Willingham Fla |
| 19 | 220th | OF Sammy Sosa Tex |
| 20 | 237th | OF Josh Hamilton Tex |
| 21 | 244th | OF Trot Nixon Cle |
| 22 | 261st | C A.J. Pierzynski ChA |
| 23 | 268th | C David Ross Cin |
| 24 | 285th | SS Ben Zobrist TB |
| 25 | 292nd | 1B Rich Aurilia SF |
| 26 | 309th | RP Jorge Julio Col |
| 27 | 316th | SP Orlando Hernandez NYN |
| 28 | 333rd | SP Russ Ortiz SF |
| 29 | 340th | SS Jason Bartlett Min |