| Round | Overall | Player |
|---|---|---|
| 1 | 3rd | 3B Alex Rodriguez NYA |
| 2 | 22nd | OF Justin Upton Ari |
| 3 | 27th | SP Dan Haren LAA |
| 4 | 46th | 1B Joey Votto Cin |
| 5 | 51st | 2B Brandon Phillips Cin |
| 6 | 70th | SP Javier Vazquez Fla |
| 7 | 75th | OF Carlos Beltran NYN |
| 8 | 94th | OF Josh Hamilton Tex |
| 9 | 99th | RP Heath Bell SD |
| 10 | 118th | SS Alexei Ramirez ChA |
| 11 | 123rd | SP Scott Baker Min |
| 12 | 142nd | RP Huston Street Col |
| 13 | 147th | C Geovany Soto ChN |
| 14 | 166th | SP Brandon Webb Tex |
| 15 | 171st | SP Stephen Strasburg Was |
| 16 | 190th | SP Randy Wolf Mil |
| 17 | 195th | RP Neftali Feliz Tex |
| 18 | 214th | OF Nolan Reimold Bal |
| 19 | 219th | SP Ben Sheets Oak |
| 20 | 238th | 3B Mark Teahen ChA |
| 21 | 243rd | OF J.D. Drew Bos |
| 22 | 262nd | SP Madison Bumgarner SF |
| 23 | 267th | SP Chris Volstad Fla |
| 24 | 286th | 2B Scott Sizemore Det |
| 25 | 291st | DH Hideki Matsui Oak |
| 26 | 310th | SP Ian Snell Sea |