| Round | Overall | Player |
|---|---|---|
| 1 | 8th | 1B Ryan Howard Phi |
| 2 | 17th | SP Tim Lincecum SF |
| 3 | 32nd | OF Nick Markakis Bal |
| 4 | 41st | OF Jason Bay NYN |
| 5 | 56th | OF Alexis Rios ChA |
| 6 | 65th | SS Derek Jeter NYA |
| 7 | 80th | 3B Ryan Zimmerman Was |
| 8 | 89th | SP Felix Hernandez Sea |
| 9 | 104th | SP Ricky Nolasco Fla |
| 10 | 113th | SP Scott Kazmir LAA |
| 11 | 128th | RP Joakim Soria KC |
| 12 | 137th | RP Bobby Jenks ChA |
| 13 | 152nd | C Jorge Posada NYA |
| 14 | 161st | DH Pat Burrell TB |
| 15 | 176th | RP Brandon Morrow Sea |
| 16 | 185th | RP Francisco Cordero Cin |
| 17 | 200th | SP Randy Johnson Ret |
| 18 | 209th | 2B Akinori Iwamura Pit |
| 19 | 224th | 2B Jed Lowrie Bos |
| 20 | 233rd | 1B Billy Butler KC |
| 21 | 248th | OF Jeremy Hermida Bos |
| 22 | 257th | OF Denard Span Min |
| 23 | 272nd | OF David DeJesus KC |
| 24 | 281st | C Dioner Navarro TB |
| 25 | 296th | SP Sean Marshall ChN |
| 26 | 305th | SP Rick Porcello Det |
| 27 | 320th | 3B Brandon Wood LAA |
| 28 | 329th | SS Erick Aybar LAA |
| 29 | 344th | SP Barry Zito SF |