| Round | Overall | Player |
|---|---|---|
| 1 | 3rd | 1B Ryan Howard Phi |
| 2 | 22nd | OF Carlos Beltran NYN |
| 3 | 27th | 1B Lance Berkman Hou |
| 4 | 46th | OF Alexis Rios Tor |
| 5 | 51st | RP J.J. Putz Sea |
| 6 | 70th | RP Mariano Rivera NYA |
| 7 | 75th | SP Aaron Harang Cin |
| 8 | 94th | SS Miguel Tejada Hou |
| 9 | 99th | OF Andruw Jones LAD |
| 10 | 118th | SP John Smoltz Bos |
| 11 | 123rd | SP Bronson Arroyo Cin |
| 12 | 142nd | 3B Alex Gordon KC |
| 13 | 147th | SP Derek Lowe Atl |
| 14 | 166th | 2B Mark Ellis Oak |
| 15 | 171st | SP Jon Garland Ari |
| 16 | 190th | SP Andy Pettitte NYA |
| 17 | 195th | OF J.D. Drew Bos |
| 18 | 214th | SP Jeff Suppan Mil |
| 19 | 219th | C Ben Molina SF |
| 20 | 238th | SP Aaron Cook Col |
| 21 | 243rd | RP Troy Percival TB |
| 22 | 262nd | 2B Felipe Lopez Was |
| 23 | 267th | OF Jack Cust Oak |
| 24 | 286th | 3B Jose Bautista Pit |
| 25 | 291st | 2B Luis Castillo NYN |
| 26 | 310th | OF Steven Pearce Pit |
| 27 | 315th | C Ryan Doumit Pit |
| 28 | 334th | SP John Patterson Tex |
| 29 | 339th | OF Michael Bourn Hou |