| Round 1 |
| Pick | Team
| Player | Affiliation | Position | Age | Ht | Wt | City | State | Country |
| 1 |  | Chance Myers | California - Los Angeles | D | 20 | 6'0 | 160 | Thousand Oaks | CA | USA |
| Pick comment: Acquired from the San Jose Earthquakes. |
| 2 |  | Brek Shea | U-17 National Team | M/D | 17 | 6'3 | 180 | College Station | TX | USA |
| Pick comment: Acquired from Toronto FC. |
| 3 |  | Anthony Beltran | California - Los Angeles | M/D | 20 | 5'8 | 150 | Claremont | CA | USA |
| 4 |  | Sean Franklin | California State Northridge | M/D | 22 | 5'10 | 155 | Palmdale | CA | USA |
| 5 |  | Ciaran O'Brien | California - Santa Barbara | M | 20 | 5'9 | 150 | Tacoma | WA | USA |
| 6 |  | Andy Iro | California - Santa Barbara | D | 23 | 6'5 | 205 | Liverpool, England | | England |
| 7 |  | Patrick Nyarko | Virginia Tech | F | 21 | 6'0 | 165 | Kumasi, Ghana | | Ghana |
| Pick comment: Acquired from the New York Red Bulls. |
| 8 | | Josh Lambo | U-17 National Team | GK | 17 | 6'0 | 206 | Middleton | WI | USA |
| 9 |  | Julius James | Connecticut | D | 23 | 6'0 | 180 | Maloney Gardens, Trinidad | | Trinidad |
| Pick comment: Acquired from Chivas USA. |
| 10 | | Pat Phelan | Wake Forest | M | 22 | 6'1 | 175 | Enfield | CT | USA |
| Pick comment: Acquired from D.C. United. |
| 11 | | Roger Espinoza | Ohio State | M/D | 21 | 5'11 | 160 | Aurora | CO | USA |
| 12 | | Dominic Cervi | Tulsa | GK | 21 | 6'6 | 205 | Norman | OK | USA |
| 13 |  | Rob Valentino | San Francisco | D | 22 | 6'3 | | Cave Creek | AZ | USA |
| 14 | | David Horst | Old Dominion | D | 22 | 6'4 | 200 | Pine Grove | PA | USA |
| Pick comment: Acquired from Toronto FC. The pick originally belonged to the Houston Dynamo. |
| Round 2 |
| Pick | Team
| Player | Affiliation | Position | Age | Ht | Wt | City | State | Country |
| 15 |  | Shea Salinas | Furman | M | 21 | 5'10 | 150 | Grapevine | TX | USA |
| 16 |  | Eric Brunner | Ohio State | D | 21 | 6'4 | 170 | Dublin | OH | USA |
| Pick comment: Acquired from Toronto FC. |
| 17 | | Alex Nimo | U-17 National Team | M | 17 | 5'5 | 142 | Portland | OR | USA |
| 18 | | Michael Videira | Duke | M | 22 | 5'10 | 175 | Milford | MA | USA |
| Pick comment: Acquired from the Los Angeles Galaxy. |
| 19 | | Eric Avila | California - Santa Barbara | M | 20 | 5'8 | 150 | San Diego | CA | USA |
| Pick comment: Acquired from the Colorado Rapids. |
| 20 | | George Josten | Gonzaga | F/M | 21 | 6'0 | 180 | Idaho Falls | ID | USA |
| 21 | | Ely Allen | Washington | F | 21 | 5'11 | 165 | Kent | WA | USA |
| Pick comment: Acquired from the New York Red Bulls. |
| 22 | | Ricardo Pierre-Louis | Lee | F | 23 | 6'1 | 177 | Leogane, Haite | | Haiti |
| Pick comment: Acquired from FC Dallas. |
| 23 | | Yomby William | Old Dominion | D | 26 | 6'4 | 185 | Bafoussam, Cameroon | | Cameroon |
| Pick comment: Acquired from Chivas USA. |
| 24 |  | Andrew Jacobson | California - Berkeley | M | 22 | 6'2 | 188 | Palo Alto | CA | USA |
| 25 | | Jonathan Leathers | Furman | D | 22 | 5'9 | 160 | Athens | GA | USA |
| Pick comment: Acquired from the Los Angeles Galaxy. The pick originally belonged to the Kansas City Wizards. |
| 26 | | Peter Lowry | Santa Clara | M | 22 | 5'11 | 165 | Fair Oaks | CA | USA |
| 27 | | Joe Germanese | Duke | M | 22 | 5'10 | 163 | St. Louis | MO | USA |
| 28 | | Brian Edwards | Wake Forest | GK | 23 | 6'3 | 195 | Charlotte | NC | USA |
| Pick comment: Acquired from the Los Angeles Galaxy. The pick originally belonged to the Houston Dynamo. |
| Round 3 |
| Pick | Team
| Player | Affiliation | Position | Age | Ht | Wt | City | State | Country |
| 29 | | Julian Valentin | Wake Forest | D | 20 | 6'0 | 180 | Lancaster | PA | USA |
| Pick comment: Acquired from the San Jose Earthquakes. |
| 30 | | Mike Zaher | California - Los Angeles | D | 22 | 5'10 | 165 | Las Vegas | NV | USA |
| 31 | | Ryan Miller | Notre Dame | D | 23 | 5'11 | 165 | Barrington | IL | USA |
| Pick comment: Acquired from FC Dallas. |
| 32 | | Luke Sassano | California - Berkeley | M/D | 22 | 6'1 | 175 | Huber Heights | OH | USA |
| Pick comment: Acquired from the Los Angeles Galaxy. |
| 33 | | Ryan Cordeiro | Connecticut | F | 21 | 5'11 | 175 | Highland Mills | NY | USA |
| Pick comment: Acquired from the Colorado Rapids. |
| 34 | | Matt Allen | Creighton | GK | 21 | 6'3 | 210 | Omaha | NE | USA |
| Pick comment: Acquired from the Columbus Crew. |
| 35 | | Joseph Lapira | Notre Dame | F | 21 | 5'8 | 150 | Lake Charles | LA | USA |
| Pick comment: Acquired from the Colorado Rapids. The pick originally belonged to the New York Red Bulls. |
| 36 | | Adrian Chevannes | Southern Methodist | D | 21 | 5'10 | 175 | Fort Worth | TX | USA |
| Pick comment: Acquired from FC Dallas. |
| 37 | | Brennan Tennelle | California - Santa Barbara | M | | 5'11 | 150 | San Diego | CA | USA |
| Pick comment: Acquired from Chivas USA. |
| 38 | | Dwight Barnett | Lynn | F | | 6'1 | 180 | Jamaica | NY | USA |
| Pick comment: Acquired from D.C. United. |
| 39 | | Matt Marquess | Santa Clara | D | 21 | 6'0 | 170 | Palo Alto | CA | USA |
| 40 | | Stephen King | Maryland | M | 21 | 5'8 | 153 | Medford | NJ | USA |
| 41 | | Matthew Britner | Brown | D | 22 | 6'0 | 180 | Halifax, Nova Scotia | | Canada |
| 42 |  | Geoff Cameron | Rhode Island | M | 22 | 6'3 | 185 | Attleboro | MA | USA |
| Round 4 |
| Pick | Team
| Player | Affiliation | Position | Age | Ht | Wt | City | State | Country |
| 43 |  | Keith Savage | West Florida | M | 22 | 6'2 | 185 | Gulf Breeze | FL | USA |
| Pick comment: Acquired from the San Jose Earthquakes. |
| 44 | | David Roth | Northwestern | M | 22 | 5'8 | 138 | Saint Louis | MO | USA |
| Pick comment: Acquired from Toronto FC. |
| 45 | | Jamil Roberts | California - Santa Clara | D | | 6'0 | 175 | Fremont | CA | USA |
| Pick comment: Acquired from Real Salt Lake. |
| 46 | | Brandon McDonald | San Francisco | F | | 6'1 | 185 | Glendale | AZ | USA |
| 47 | | Brian Grazier | Saint Louis | M | 21 | 6'0 | 175 | Edwardsville | IL | USA |
| 48 | | Steven Lenhart | Azusa Pacific | F | | 6'1 | | Yorba Linda | CA | USA |
| 49 | | Scott Campbell | North Carolina | M | 21 | 5'10 | 160 | Plantation | FL | USA |
| Pick comment: Acquired from the New York Red Bulls. |
| 50 | | Ben Nason | Virginia Tech | M | | 5'10 | 180 | Stafford | VA | USA |
| 51 | | Matt Hatzke | Santa Clara | M/D | 22 | 5'9 | 155 | San Jose | CA | USA |
| Pick comment: Acquired from the New York Red Bulls. The pick originally belonged to Chivas USA who gave the pick to Real Salt Lake. |
| 52 | | Tony Schmitz | Creighton | D/M | | 6'0 | 180 | Omaha | NE | USA |
| 53 | | Rauwshan McKenzie | Michigan State | D | 21 | 6'1 | 185 | Hoffman Estates | IL | USA |
| 54 | | Austin Washington | Gonzaga | D | 22 | 6'0 | | Spokane | WA | USA |
| 55 | | Spencer Wadsworth | Duke | M | | 5'8 | 160 | Dallas | TX | USA |
| 56 | | Jeremy Barlow | Virginia | M | 22 | 5'8 | 155 | Herndon | VA | USA |
