| Round | Overall | Player |
|---|---|---|
| 1 | 6th | OF Barry Bonds SF |
| 2 | 19th | C Mike Piazza NYN |
| 3 | 30th | 2B Bret Boone Sea |
| 4 | 43rd | 1B Jeff Bagwell Hou |
| 5 | 54th | 2B Kazuo Matsui NYN |
| 6 | 67th | 3B Morgan Ensberg Hou |
| 7 | 78th | SP Andy Pettitte Hou |
| 8 | 91st | SP Esteban Loaiza NYA |
| 9 | 102nd | OF Torii Hunter Min |
| 10 | 115th | SP Tom Glavine NYN |
| 11 | 126th | SP C.C. Sabathia Cle |
| 12 | 139th | RP Braden Looper NYN |
| 13 | 150th | SP Brett Myers Phi |
| 14 | 163rd | SS Khalil Greene SD |
| 15 | 174th | SP Zack Greinke KC |
| 16 | 187th | OF Rocco Baldelli TB |
| 17 | 198th | SP Jae Weong Seo NYN |
| 18 | 211th | 1B John Olerud NYA |
| 19 | 222nd | 1B Justin Morneau Min |
| 20 | 235th | DH Edgar Martinez Sea |
| 21 | 246th | OF Mike Cameron NYN |
| 22 | 259th | 2B Chase Utley Phi |
| 23 | 270th | SP Kazuhisa Ishii LA |
| 24 | 283rd | SP Chin-Hui Tsao Col |
| 25 | 294th | SS Omar Vizquel Cle |
| 26 | 307th | OF Jerry Hairston Jr. Bal |
| 27 | 318th | SP Josh Fogg Pit |
| 28 | 331st | OF Craig Biggio Hou |
| 29 | 342nd | 2B Eric Young Tex |