| Round | Overall | Player |
|---|---|---|
| 1 | 9th | 1B Prince Fielder Mil |
| 2 | 16th | 3B Mark Reynolds Bal |
| 3 | 33rd | 1B Adam Lind Tor |
| 4 | 40th | OF Manny Ramirez ChA |
| 5 | 57th | OF Raul Ibanez Phi |
| 6 | 64th | C Matt Wieters Bal |
| 7 | 81st | SS Stephen Drew Ari |
| 8 | 88th | SP Jake Peavy ChA |
| 9 | 105th | SP Jair Jurrjens Atl |
| 10 | 112th | RP David Aardsma Sea |
| 11 | 129th | RP Trevor Hoffman Ret |
| 12 | 136th | OF Alfonso Soriano ChN |
| 13 | 153rd | RP Leo Nunez Fla |
| 14 | 160th | 2B Rickie Weeks Mil |
| 15 | 177th | 1B Todd Helton Col |
| 16 | 184th | C Mike Napoli LAA |
| 17 | 201st | SP Daisuke Matsuzaka Bos |
| 18 | 208th | SP Joel Pineiro LAA |
| 19 | 225th | OF Austin Jackson Det |
| 20 | 232nd | 3B Martin Prado Atl |
| 21 | 249th | SP Aroldis Chapman Cin |
| 22 | 256th | SS J.J. Hardy Bal |
| 23 | 273rd | SP Randy Wells ChN |
| 24 | 280th | SP Kevin Millwood Bal |
| 25 | 297th | 3B Casey Blake LAD |
| 26 | 304th | SP Zach Duke Ari |
| 27 | 321st | OF Drew Stubbs Cin |
| 28 | 328th | SP Erik Bedard Sea |
| 29 | 345th | OF Josh Willingham Was |