| round 1 |
| Pick | Team
| Player | Affiliation | Position | Age | Ht | Wt | City | State | Country |
| 1 |  | Marvell Wynne | UCLA | D | 19 | 5'9 | 171 | Poway | CA | USA |
| Pick comment: Acquired from Chivas USA in exchange for the No. 5 pick in the 2006 SuperDraft and defender Jason Hernandez. |
| 2 |  | Mehdi Ballouchy | Santa Clara | M | 22 | 5'11 | 165 | Casablanca | | Morocco |
| 3 |  | Jason Garey | Maryland | F | 21 | 6'0 | 180 | Gonzales | LA | USA |
| 4 |  | Yura Movsisyan | Pasadena City College | F | 18 | 6'0 | 180 | Baku | | Azerbajian |
| 5 |  | Sacha Kljestan | Seton Hall | F | 20 | 6'1 | 150 | Huntington Beach | CA | USA |
| Pick comment: Acquired from MetroStars, along with defender Jason Hernandez, in exchange for No. 1 pick. |
| 6 |  | Dax McCarty | North Carolina | M | 18 | 5'9 | 142 | Winter Park | FL | USA |
| 7 |  | Justin Moose | Wake Forest | M | 22 | 5'8 | 145 | Statesville | NC | USA |
| 8 |  | Patrick Ianni | UCLA | D | 20 | 6'1 | 175 | Lodi | CA | USA |
| 9 | | Kei Kamara | Cal State Dominguez Hills | F | 21 | 6'2 | 165 | Lawndale | CA | USA |
| Pick comment: Acquired from Colorado Rapids |
| 10 |  | Calen Carr | California | F | 23 | 6'0 | 150 | Berkeley | CA | USA |
| 11 |  | Leandro de Oliveira | Alabama - Birmingham | M | 23 | 5'8 | 155 | Bryan | TX | USA |
| 12 |  | Nathan Sturgis | Clemson | D-M | 18 | 5'10 | 150 | St. Augustine | FL | USA |
| round 2 |
| Pick | Team
| Player | Affiliation | Position | Age | Ht | Wt | City | State | Country |
| 13 | | Jed Zayner | Indiana | D | 21 | 5'11 | 165 | Orland Park | IL | USA |
| Pick comment: Acquired from New England Revolution, who originally received it from Chivas USA. |
| 14 | | Jeff Curtin | Georgetown | D | 22 | 6'3 | 190 | Oreland | PA | USA |
| Pick comment: Acquired from Real Salt Lake. |
| 15 | | Justin Moore | Clemson | D-M | 22 | 6'0 | 177 | Snellville | GA | USA |
| Pick comment: Acquired from Columbus Crew. |
| 16 | | Lance Watson | New Mexico | M | 22 | 5'7 | 150 | Nederland | TX | USA |
| 17 | | Josmer Altidore | U.S. Under-17 | F | 16 | 5'10 | 175 | Boca Raton | FL | USA |
| Pick comment: Acquired from Real Salt Lake. Originally the MetroStars pick. |
| 18 | | Blake Wagner | U.S. Under-17 | D-M | 17 | 5'10 | 160 | Tampa | FL | USA |
| 19 | | Tyson Wahl | California | D | 21 | 6'2 | 185 | Newport Beach | CA | USA |
| Pick comment: Acquired from Chicago Fire, who originally received it from D.C. United. |
| 20 | | Brian Plotkin | Indiana | M | 21 | 5'9 | 150 | Lisle | IL | USA |
| Pick comment: Acquired from Houston. |
| 21 |  | Jacob Peterson | Indiana | F | 19 | 5'10 | 160 | Portage | MI | USA |
| 22 | | Dominic Oduro | Virginia Commonwealth | F | 20 | 6'0 | 155 | Pramso | | Ghana |
| Pick comment: Acquired from Chicago Fire, who forfeited the pick due to conditional agreement. |
| 23 | | Willie Sims | Cal State Northridge | F | 21 | 5'9 | 150 | Los Angeles | CA | USA |
| 24 | | Marc Burch | Maryland | F | | 6'2 | 190 | Cincinnati | OH | USA |
| round 3 |
| Pick | Team
| Player | Affiliation | Position | Age | Ht | Wt | City | State | Country |
| 25 | | Kyle Veris | Ohio State | D | 21 | 6'3 | 170 | Strongsville | OH | USA |
| Pick comment: Acquired from Chivas USA. |
| 26 | | Ryan Johnson | Oregon State | F-M | 21 | 6'1 | 180 | Boston | MA | Jamaica |
| 27 | | Brandon Moss | New Mexico | M | 21 | 6'1 | 185 | Albuquerque | NM | USA |
| 28 | | Matt Groenwald | St. John's | M | 22 | 5'8 | 173 | Mt. Prospect | IL | USA |
| 29 | | Stephen Shirley | Virginia Commonwealth | D-M | 22 | 5'10 | 165 | Carrollton | TX | USA |
| Pick comment: Acquired from MetroStars. |
| 30 | | Ray Burse, Jr | Ohio State | GK | 21 | 6'1 | 185 | Prospect | KY | USA |
| 31 | | Rod Dyachenko | UNLV | M | 22 | 6'0 | 165 | Vancouver | WA | USA |
| 32 | | Andre Schmid | St. John's | F | 22 | 6'4 | 200 | Sacramento | CA | USA |
| 33 | | Dayton O'Brien | Memphis | M-F | 22 | 5'11 | 155 | Memphis | TN | USA |
| Pick comment: Acquired from the Colorado Rapids, along with a conditional pick in the 2007 MLS SuperDraft, in exchange for goalkeeper Matt Jordan and defender Chris Wingert. |
| 34 | | Jordan Russolillo | Southern Connecticut | D | 21 | 5'11 | 165 | Middletown | CT | USA |
| 35 | | Kyle Brown | Tulsa | F | 22 | 5'11 | 165 | Southlake | TX | USA |
| 36 | | Chris Dunsheath | Bradley | GK | 22 | 6'3 | 196 | Rockford | IL | USA |
| round 4 |
| Pick | Team
| Player | Affiliation | Position | Age | Ht | Wt | City | State | Country |
| 37 | | Jonathan Bornstein | UCLA | F | 21 | 5'9 | 145 | Los Alamitos | CA | USA |
| 38 | | Duke Hashimoto | Southern Methodist | F | 21 | 5'7 | 150 | Kapolei | HI | USA |
| Pick comment: Acquired from FC Dallas, who acquired it from Real Salt Lake, in exchange for the Crew's 2007 natural third-round SuperDraftpick. |
| 39 | | Jeff Carroll | St. John's | M-D | 21 | 5'10 | 160 | Springfield | VA | USA |
| Pick comment: Acquired from Columbus Crew. |
| 40 | | Eric Kronberg | California | GK | 22 | 6'5 | 210 | Santa Rosa | CA | USA |
| 41 | | Blake Camp | Duke | M | 22 | 6'2 | 194 | Danielsville | GA | USA |
| Pick comment: Acquired from Houston, which originally received it from the MetroStars, in exchange for goalkeeper Zach Wells. |
| 42 | | Michael Dello-Russo | Maryland | M | 22 | 5'10 | 165 | Columbia | MD | USA |
| 43 | | Mike Ambersley | Indiana | F | 22 | 5'7 | 155 | Ballwin | MO | USA |
| Pick comment: Acquired from DC United. |
| 44 | | Mike Chabala | Washington | M | 21 | 6'0 | 178 | Fresno | CA | USA |
| 45 | | Josh Brown | New Mexico | D | 22 | 6'2 | 180 | Portland | OR | USA |
| 46 | | Jeremy Ashe | Marshall | M | 22 | 5'10 | 170 | Cinnaminson | NJ | USA |
| 47 | | Kenney Bertz | Maryland | D | 22 | 6'1 | 195 | Liberty Township | OH | USA |
| Pick comment: Acquired from New England Revolution. |
| 48 | | Aaron King | NC State | F | 21 | 6'0 | 175 | Denver | CO | USA |
