| Round | Overall | Player |
|---|---|---|
| 1 | 2nd | 3B Alex Rodriguez NYA |
| 2 | 23rd | SS Jimmy Rollins Phi |
| 3 | 26th | OF Bobby Abreu NYA |
| 4 | 47th | C Victor Martinez Cle |
| 5 | 50th | 1B Carlos Delgado NYN |
| 6 | 71st | RP Huston Street Oak |
| 7 | 74th | SP John Smoltz Atl |
| 8 | 95th | OF Nick Swisher ChA |
| 9 | 98th | OF Barry Bonds SF |
| 10 | 119th | SP Anibal Sanchez Fla |
| 11 | 122nd | OF Nick Markakis Bal |
| 12 | 143rd | SS Jhonny Peralta Cle |
| 13 | 146th | SP Chris Capuano Mil |
| 14 | 167th | SP Jake Westbrook Cle |
| 15 | 170th | RP Brian Fuentes Col |
| 16 | 191st | RP Joe Borowski Cle |
| 17 | 194th | SP Jon Garland LAA |
| 18 | 215th | OF Gary Matthews Jr. LAA |
| 19 | 218th | SP Cliff Lee Cle |
| 20 | 239th | OF Luke Scott Bal |
| 21 | 242nd | 1B Mike Jacobs Fla |
| 22 | 263rd | 2B Kazuo Matsui Hou |
| 23 | 266th | 2B Akinori Iwamura TB |
| 24 | 287th | OF Andre Ethier LAD |
| 25 | 290th | 1B Ryan Garko Cle |
| 26 | 311th | C Johnny Estrada NYN |
| 27 | 314th | SP Matt Garza TB |
| 28 | 335th | 2B Craig Biggio Hou |
| 29 | 338th | OF Corey Patterson Bal |