| Round | Overall | Player |
|---|---|---|
| 1 | 2nd | SS Hanley Ramirez Fla |
| 2 | 23rd | 3B Mark Reynolds Bal |
| 3 | 26th | SP Tim Lincecum SF |
| 4 | 47th | C Matt Wieters Bal |
| 5 | 50th | SP Josh Beckett Bos |
| 6 | 71st | 2B Aaron Hill Tor |
| 7 | 74th | SP Josh Johnson Fla |
| 8 | 95th | OF Nick Markakis Bal |
| 9 | 98th | OF Lance Berkman STL |
| 10 | 119th | RP Trevor Hoffman Ret |
| 11 | 122nd | OF Alfonso Soriano ChN |
| 12 | 143rd | OF Carlos Quentin ChA |
| 13 | 146th | 1B Todd Helton Col |
| 14 | 167th | SP Max Scherzer Det |
| 15 | 170th | RP Francisco Cordero Cin |
| 16 | 191st | SP Clay Buchholz Bos |
| 17 | 194th | SS Erick Aybar LAA |
| 18 | 215th | 2B Orlando Hudson Min |
| 19 | 218th | SP Johnny Cueto Cin |
| 20 | 239th | 1B Lyle Overbay Tor |
| 21 | 242nd | 3B Mark Teahen ChA |
| 22 | 263rd | SP Scott Feldman Tex |
| 23 | 266th | OF Colby Rasmus StL |
| 24 | 287th | OF Rajai Davis Oak |
| 25 | 290th | C Buster Posey SF |
| 26 | 311th | RP Matt Lindstrom Col |
| 27 | 314th | OF Kosuke Fukudome ChN |
| 28 | 335th | OF Nate Schierholtz SF |
| 29 | 338th | 2B Chris Getz KC |