| Round | Overall | Player |
|---|---|---|
| 1 | 9th | 3B Evan Longoria TB |
| 2 | 16th | SS Troy Tulowitzki Col |
| 3 | 33rd | OF Justin Upton Ari |
| 4 | 40th | 1B Justin Morneau Min |
| 5 | 57th | SP Dan Haren LAA |
| 6 | 64th | 2B Robinson Cano NYA |
| 7 | 81st | 1B Carlos Pena ChN |
| 8 | 88th | SP Chris Carpenter StL |
| 9 | 105th | SP Jake Peavy ChA |
| 10 | 112th | OF Andrew McCutchen Pit |
| 11 | 129th | SP John Lackey Bos |
| 12 | 136th | OF Nate McLouth Atl |
| 13 | 153rd | 1B Brad Hawpe SD |
| 14 | 160th | SP Jair Jurrjens Atl |
| 15 | 177th | RP David Aardsma Sea |
| 16 | 184th | 3B Ian Stewart Col |
| 17 | 201st | C Chris Iannetta Col |
| 18 | 208th | 2B Rickie Weeks Mil |
| 19 | 225th | SP Ervin Santana LAA |
| 20 | 232nd | OF Julio Borbon Tex |
| 21 | 249th | SP Ben Sheets Oak |
| 22 | 256th | OF Garrett Jones Pit |
| 23 | 273rd | SS Ian Desmond Was |
| 24 | 280th | 1B Matt LaPorta Cle |
| 25 | 297th | SP Homer Bailey Cin |
| 26 | 304th | SP Philip Hughes NYA |
| 27 | 321st | OF Kyle Blanks SD |
| 28 | 328th | C John Baker Fla |
| 29 | 345th | OF Delmon Young Min |