| Round | Overall | Player |
|---|---|---|
| 1 | 3rd | SS Troy Tulowitzki Col |
| 2 | 22nd | DH Adam Dunn ChA |
| 3 | 27th | OF Jose Bautista Tor |
| 4 | 46th | SP Matt Cain SF |
| 5 | 51st | SP Trevor Cahill Ari |
| 6 | 70th | OF Chris Young Ari |
| 7 | 75th | SP Roy Oswalt Phi |
| 8 | 94th | 2B Kelly Johnson Tor |
| 9 | 99th | SP Daniel Hudson Ari |
| 10 | 118th | DH Vladimir Guerrero Bal |
| 11 | 123rd | RP Francisco Cordero Cin |
| 12 | 142nd | OF Andres Torres NYN |
| 13 | 147th | SP Ervin Santana LAA |
| 14 | 166th | 1B Aubrey Huff SF |
| 15 | 171st | SP Roberto Hernandez Cle |
| 16 | 190th | OF Jason Kubel Ari |
| 17 | 195th | SP Ian Kennedy Ari |
| 18 | 214th | 2B Danny Espinosa Was |
| 19 | 219th | SP Ivan Nova NYA |
| 20 | 238th | OF Travis Snider Tor |
| 21 | 243rd | 2B Jose Lopez Cle |
| 22 | 262nd | OF Garrett Jones Pit |
| 23 | 267th | 3B Danny Valencia Min |
| 24 | 286th | C A.J. Pierzynski ChA |
| 25 | 291st | SP Mike Leake Cin |
| 26 | 310th | SS Yuniesky Betancourt KC |
| 27 | 315th | RP Fernando Rodney TB |
| 28 | 334th | C Alex Avila Det |
| 29 | 339th | RP Jonny Venters Atl |