| Round 1 | |||||
| 1 | Philadelphia | Andre Blake | GK | Connecticut | |
| 2 | D.C. United | Steve Birnbaum | D | California | |
| 3 | Vancouver | Christian Dean | D | California | |
| 4 | New England | Steve Neumann | F | Georgetown | |
| 5 | Montreal | Eric Miller | D | Creighton | |
| 6 | F.C. Dallas | Tesho Akindele | F | Colorado School of Mines | |
| 7 | Vancouver | Andre Lewis | M | Portmore United | |
| 8 | Seattle | Damion Lowe | D | Hartford | |
| 9 | San Jose | J.J. Koval | M | Stanford | |
| 10 | Toronto | Nick Hagglund | D | Xavier | |
| 11 | New England | Patrick Mullins | F | Maryland | |
| 12 | Colorado | Marlon Hairston | M | Louisville | |
| 13 | Chicago | Marco Franco | D | UC Irvine | |
| 14 | Columbus | Ben Sweat | D | South Florida | |
| 15 | Philadelphia | Pedro Ribeiro | M | Coastal Carolina | |
| 16 | Houston | AJ Cochran | D | Wisconsin | |
| 17 | Portland | Schillo Tshuma | F | Maryland | |
| 18 | Salt Lake | Ryan Neil | D | California | |
| 19 | Colorado | Grant Van De Casteele | D | Notre Dame | |
| Round 2 | |||||
| 20 | Chivas | Thomas McNamara | M | Clemson | |
| 21 | Seattle | Jimmy Ockford | D | Louisville | |
| 22 | New York | Chris Duvall | D | Wake Forest | |
| 23 | Los Angeles | Kyle Venter | D | New Mexico | |
| 24 | Toronto | Daniel Lovitz | M | Elon | |
| 25 | Philadelphia | Kevin Cope | D | Michigan State | |
| 26 | Portland | Taylor Peay | D | Washington | |
| 27 | Philadelphia | Robert Derschang | D | Akron | |
| 28 | San Jose | Joe Sofia | D | UCLA | |
| 29 | D.C. United | Victor Munoz | M | UCLA | |
| 30 | Vancouver | Mamadou Diouf | F | Connecticut | |
| 31 | New England | Alec Sundly | M | California | |
| 32 | Houston | Mark Sherrod | F | Memphis | |
| 33 | Colorado | Jared Watts | M | Wake Forest | |
| 34 | New York | Eric Stevenson | M | Akron | |
| 35 | Colorado | John Berner | GK | SIUE | |
| 36 | Portland | Aaron Long | M | UC Riverside | |
| 37 | Montreal | George Malki | M | Cal Poly | |
| 38 | Kansas City | Adnan Gabeljic | F | Saint Louis | |
