| Round | Overall | Player |
|---|---|---|
| 1 | 9th | C Joe Mauer Min |
| 2 | 16th | 3B David Wright NYN |
| 3 | 33rd | 2B Dan Uggla Atl |
| 4 | 40th | 1B Joey Votto Cin |
| 5 | 57th | OF Curtis Granderson NYA |
| 6 | 64th | SP Josh Johnson Fla |
| 7 | 81st | 2B Brandon Phillips Cin |
| 8 | 88th | SP Wandy Rodriguez Hou |
| 9 | 105th | SP Javier Vazquez Fla |
| 10 | 112th | OF Alfonso Soriano ChN |
| 11 | 129th | SP Rick Porcello Det |
| 12 | 136th | OF Nate McLouth Atl |
| 13 | 153rd | SP John Danks ChA |
| 14 | 160th | SP Gavin Floyd ChA |
| 15 | 177th | SP Brian Matusz Bal |
| 16 | 184th | SS Alexei Ramirez ChA |
| 17 | 201st | RP Chad Qualls TB |
| 18 | 208th | OF Chris Young Ari |
| 19 | 225th | SS Ryan Theriot STL |
| 20 | 232nd | OF Magglio Ordonez Det |
| 21 | 249th | RP Leo Nunez Fla |
| 22 | 256th | RP Matt Lindstrom Col |
| 23 | 273rd | 3B Garrett Atkins Pit |
| 24 | 280th | SP Jake Westbrook STL |
| 25 | 297th | OF Milton Bradley Sea |
| 26 | 304th | 1B Daric Barton Oak |
| 27 | 321st | OF Franklin Gutierrez Sea |
| 28 | 328th | 2B Akinori Iwamura Pit |
| 29 | 345th | C Gregg Zaun Mil |