First Round
| 1. San Jose | Chris Carrieri |
| 2. Tampa Bay | Ali Curtis |
| 3. D.C. United | Mark Lisi |
| 4. D.C. United | Ryan Nelsen |
| 5. Dallas | Joselito Vaca |
| 6. Tampa Bay | Craig Demmin |
| 7. Dallas | Ryan Suarez |
| 8. D.C. United | Santino Quaranta |
| 9. Los Angeles | Brian Mullan |
| 10. Columbus | Duncan Oughton |
| 11. Los Angeles | Isaias Bardales |
| 12. Kansas City | Jose Burciaga |
| Second Round | |
| 1. MetroStars | Rodrigo Faria |
| 2. Tampa Bay | Devin Barclay |
| 3. D.C. United | Bryan Namoff |
| 4. Los Angeles | Brian Ching |
| 5. Colorado | Steven Herdsmann |
| 6. Miami | Ali Ngon |
| 7. Dallas | Edward Johnson |
| 8. San Jose | Edward Robinson |
| 9. New England | Nick Downing |
| 10. Los Angeles | Robert Russell |
| 11. Chicago | Justin Evans |
| 12. Kansas City | Andrew Gregor |
| Third Round | |
| 1. Dallas | Josue Mayard |
| 2. MetroStars | Kerwin Jemmott |
| 3. Columbus | Edson Buddle |
| 4. D.C. United | Craig Ziadie |
| 5. Chicago | Jim Curtin |
| 6. Columbus | Kevin Adams |
| 7. San Jose | Craig Waibel |
| 8. Colorado | Ryan Lee |
| 9. Chicago | Henry Ring |
| 10. Tampa Bay | Alberto Munoz |
| 11. Kansas City | Ben Stafford |
| 12. Colorado | Eric Lukin |
| Fourth Round | |
| 1. San Jose | Fabio Eidelwine |
| 2. Miami | Greg Simmonds |
| 3. Columbus | McKinley Tennyson |
| 4. Miami | Cory Gibbs |
| 5. Colorado | Ryan Trout |
| 6. New England | Yari Allnutt |
| 7. Dallas | Adam Zapala |
| 8. Tampa Bay | Adam Throop |
| 9. Los Angeles | Brent Rahim |
| 10. MetroStars | Martin Klinger |
| 11. New England | Fernando Ortiz Solis |
| 12. Kansas City | Pablo Webster |
| Fifth Round | |
| 1. San Jose | Corey Woolfolk |
| 2. D.C. United | Caleb Norkus |
| 3. Columbus | Scott Powers |
| 4. Miami | Teofilo Cubillas |
| 5. New England | Eric Pogue |
| 6. New England | Shaun Tsakiris |
| 7. Dallas | Gary DePalma |
| 8. Tampa Bay | Mersim Beskovic |
| 9. Los Angeles | Alex Bengard |
| 10. MetroStars | Oneal Peart |
| 11. Kansas City | Narciso Fernandes |
| 12. Tampa Bay | Hector Navarte |
| Sixth Round | |
| 1. San Jose | Jorge Martinez |
| 2. D.C. United | T.J. Hannig |
| 3. Columbus | Phil Karn |
| 4. Miami | Daouda Kante |
| 5. Colorado | John Carroll |
| 6. New England | Michael Feller |
| 7. Dallas | Miguel Saavedra |
| 8. Chicago | Danny Risch |
| 9. Los Angeles | Mike Potempa |
| 10. MetroStars | Russell Payne |
| 11. Chicago | Roberto Navarro |
| 12. Kansas City | Matthew Cross |