| Round | Overall | Player |
|---|---|---|
| 1 | 8th | 1B Albert Pujols StL |
| 2 | 17th | OF Alfonso Soriano ChN |
| 3 | 32nd | SP C.C. Sabathia Mil |
| 4 | 41st | SP Cole Hamels Phi |
| 5 | 56th | OF Nick Markakis Bal |
| 6 | 65th | RP Jon Papelbon Bos |
| 7 | 80th | RP Joe Nathan Min |
| 8 | 89th | 1B Ryan Garko Cle |
| 9 | 104th | OF Torii Hunter LAA |
| 10 | 113th | 3B Kevin Kouzmanoff SD |
| 11 | 128th | SP Rich Hill Bal |
| 12 | 137th | SP Jeremy Bonderman Det |
| 13 | 152nd | SS Jhonny Peralta Cle |
| 14 | 161st | SP Clay Buchholz Bos |
| 15 | 176th | OF Jose Guillen KC |
| 16 | 185th | C Ben Molina SF |
| 17 | 200th | 2B Orlando Hudson Ari |
| 18 | 209th | SP Dave Bush Mil |
| 19 | 224th | OF Austin Kearns Was |
| 20 | 233rd | SP George Sherrill Sea |
| 21 | 248th | SP Chris Carpenter StL |
| 22 | 257th | SP Micah Owings Ari |
| 23 | 272nd | 3B Pedro Feliz Phi |
| 24 | 281st | SP Manny Parra Mil |
| 25 | 296th | SS David Eckstein SD |
| 26 | 305th | 2B Kazuo Matsui Hou |
| 27 | 320th | SP Mark Mulder StL |
| 28 | 329th | C Chris Snyder Ari |
| 29 | 344th | 1B Kevin Millar Bal |