| Round | Overall | Player |
|---|---|---|
| 1 | 8th | OF Carlos Beltran NYN |
| 2 | 17th | OF Manny Ramirez Bos |
| 3 | 32nd | SS Derek Jeter NYA |
| 4 | 41st | DH Jim Thome ChA |
| 5 | 56th | 1B Jason Giambi NYA |
| 6 | 65th | 3B Chipper Jones Atl |
| 7 | 80th | SP Dontrelle Willis Det |
| 8 | 89th | RP Takashi Saito LAD |
| 9 | 104th | 1B Carlos Guillen Det |
| 10 | 113th | SP Mike Mussina NYA |
| 11 | 128th | SP Bronson Arroyo Cin |
| 12 | 137th | RP Tom Gordon Phi |
| 13 | 152nd | 2B Ian Kinsler Tex |
| 14 | 161st | RP Josh Johnson Fla |
| 15 | 176th | C Michael Barrett SD |
| 16 | 185th | SP Cliff Lee Cle |
| 17 | 200th | 1B Aubrey Huff Bal |
| 18 | 209th | SP Kei Igawa NYA |
| 19 | 224th | OF Matt Murton ChN |
| 20 | 233rd | 1B Mike Jacobs Fla |
| 21 | 248th | OF Andre Ethier LAD |
| 22 | 257th | 3B Mike Lowell Bos |
| 23 | 272nd | SP Boof Bonser Min |
| 24 | 281st | SP Matt Garza TB |
| 25 | 296th | OF Juan Rivera LAA |
| 26 | 305th | C Josh Bard SD |
| 27 | 320th | SP Taylor Tankersley Fla |
| 28 | 329th | 2B Kazuo Matsui Hou |
| 29 | 344th | SP Philip Hughes NYA |