| Round | Overall | Player |
|---|---|---|
| 1 | 12th | DH David Ortiz Bos |
| 2 | 13th | OF Grady Sizemore Cle |
| 3 | 36th | SP C.C. Sabathia Mil |
| 4 | 37th | SS Troy Tulowitzki Col |
| 5 | 60th | SP John Smoltz Bos |
| 6 | 61st | OF Nick Swisher ChA |
| 7 | 84th | SP Daisuke Matsuzaka Bos |
| 8 | 85th | C Brian McCann Atl |
| 9 | 108th | OF Kosuke Fukudome ChN |
| 10 | 109th | RP Manuel Corpas Col |
| 11 | 132nd | 3B Edwin Encarnacion Cin |
| 12 | 133rd | SP Rich Hill Bal |
| 13 | 156th | SP A.J. Burnett Tor |
| 14 | 157th | 2B Akinori Iwamura TB |
| 15 | 180th | RP Todd Jones Det |
| 16 | 181st | 1B Adam LaRoche Pit |
| 17 | 204th | 1B Billy Butler KC |
| 18 | 205th | RP Kerry Wood ChN |
| 19 | 228th | 3B Mark Reynolds Ari |
| 20 | 229th | 2B Dustin Pedroia Bos |
| 21 | 252nd | SP Zack Greinke KC |
| 22 | 253rd | SP Tim Wakefield Bos |
| 23 | 276th | OF Cameron Maybin Fla |
| 24 | 277th | OF Elijah Dukes Was |
| 25 | 300th | SS Bobby Crosby Oak |
| 26 | 301st | SP Jair Jurrjens Atl |
| 27 | 324th | SP Orlando Hernandez NYN |
| 28 | 325th | C Kurt Suzuki Oak |
| 29 | 348th | SP Andrew Miller Fla |