| Round | Overall | Player |
|---|---|---|
| 1 | 11th | SS Jimmy Rollins Phi |
| 2 | 14th | 1B Albert Pujols StL |
| 3 | 35th | 3B Garrett Atkins Col |
| 4 | 38th | 1B Justin Morneau Min |
| 5 | 59th | OF Nick Markakis Bal |
| 6 | 62nd | C Brian McCann Atl |
| 7 | 83rd | SP John Smoltz Bos |
| 8 | 86th | OF Vernon Wells Tor |
| 9 | 107th | 2B Rickie Weeks Mil |
| 10 | 110th | RP Huston Street Oak |
| 11 | 131st | SP Brett Myers Phi |
| 12 | 134th | OF Jeremy Hermida Fla |
| 13 | 155th | RP Brad Lidge Phi |
| 14 | 158th | SP Jeremy Bonderman Det |
| 15 | 179th | 2B Howie Kendrick LAA |
| 16 | 182nd | SP Bronson Arroyo Cin |
| 17 | 203rd | OF Josh Willingham Fla |
| 18 | 206th | 1B Casey Kotchman Atl |
| 19 | 227th | SP Jake Westbrook Cle |
| 20 | 230th | OF Justin Upton Ari |
| 21 | 251st | SS Bobby Crosby Oak |
| 22 | 254th | 1B Aubrey Huff Bal |
| 23 | 275th | SP Greg Maddux SD |
| 24 | 278th | C Ronny Paulino Pit |
| 25 | 299th | 3B Joe Crede ChA |
| 26 | 302nd | SP Bartolo Colon ChA |
| 27 | 323rd | SP Dave Bush Mil |
| 28 | 326th | SP Kevin Millwood Tex |
| 29 | 347th | OF Brian S. Giles SD |