| Round | Overall | Player |
|---|---|---|
| 1 | 4th | 1B Albert Pujols StL |
| 2 | 21st | OF Carlos Beltran NYN |
| 3 | 28th | SP Jake Peavy SD |
| 4 | 45th | C Russell Martin LAD |
| 5 | 52nd | 2B Brian Roberts Bal |
| 6 | 69th | 3B Mike Young Tex |
| 7 | 76th | RP Joe Nathan Min |
| 8 | 93rd | 3B Adrian Beltre Sea |
| 9 | 100th | SP Javier Vazquez ChA |
| 10 | 117th | 1B Paul Konerko ChA |
| 11 | 124th | SP Pedro Martinez NYN |
| 12 | 141st | OF Johnny Damon NYA |
| 13 | 148th | OF Jermaine Dye ChA |
| 14 | 165th | RP Takashi Saito Bos |
| 15 | 172nd | 3B Scott Rolen Tor |
| 16 | 189th | OF Jacoby Ellsbury Bos |
| 17 | 196th | SP Derek Lowe Atl |
| 18 | 213th | 2B Orlando Hudson Ari |
| 19 | 220th | RP Brad Lidge Phi |
| 20 | 237th | SP Bronson Arroyo Cin |
| 21 | 244th | SP Zack Greinke KC |
| 22 | 261st | OF Felix Pie Bal |
| 23 | 268th | 1B Mike Jacobs Fla |
| 24 | 285th | SP Chuck James Atl |
| 25 | 292nd | C Chris Snyder Ari |
| 26 | 309th | SP Chris Capuano Mil |
| 27 | 316th | SP Chris Carpenter StL |
| 28 | 333rd | 1B Nick Johnson Was |
| 29 | 340th | SS Ryan Theriot ChN |