| Round | Overall | Player |
|---|---|---|
| 1 | 4th | 2B Chase Utley Phi |
| 2 | 21st | SP C.C. Sabathia NYA |
| 3 | 28th | OF Grady Sizemore Cle |
| 4 | 45th | 3B Kevin Youkilis Bos |
| 5 | 52nd | OF Nick Markakis Bal |
| 6 | 69th | SP John Lackey Bos |
| 7 | 76th | RP Francisco Rodriguez NYN |
| 8 | 93rd | 1B Carlos Pena ChN |
| 9 | 100th | 3B Chone Figgins Sea |
| 10 | 117th | RP David Aardsma Sea |
| 11 | 124th | OF Lance Berkman STL |
| 12 | 141st | SP Scott Kazmir LAA |
| 13 | 148th | OF Carlos Gonzalez Col |
| 14 | 165th | SS Marcos Scutaro Bos |
| 15 | 172nd | C Ryan Doumit Pit |
| 16 | 189th | SP Bronson Arroyo Cin |
| 17 | 196th | OF Colby Rasmus StL |
| 18 | 213th | SS Asdrubal Cabrera Cle |
| 19 | 220th | 2B Rickie Weeks Mil |
| 20 | 237th | OF Chris Coghlan Fla |
| 21 | 244th | SP Nick Blackburn Min |
| 22 | 261st | SP Chris Young SD |
| 23 | 268th | SP Michael Pelfrey NYN |
| 24 | 285th | RP Justin Masterson Cle |
| 25 | 292nd | SP Zach Duke Ari |
| 26 | 309th | SS Ian Desmond Was |