| Round 1 |
| Pick | Team
| Player | Affiliation | Position | Age | Ht | Wt | City | State | Country |
| 1 |  | Maurice Edu | Maryland | M | 20 | 6'0 | 170 | Fontana | CA | USA |
| 2 |  | Bakary Soumare | Virginia | D | 21 | 6'4 | 190 | New York | NY | USA |
| Pick comment: Acquired from the Columbus Crew on Jan. 12, 2007 in exchange for a player to be named later. |
| 3 |  | Michael Harrington | North Carolina | D | 20 | 6'0 | 170 | Greenville | NC | USA |
| 4 |  | Chris Seitz | Maryland, U20 National Team | GK | 19 | 6'4 | 210 | San Luis Obispo | CA | USA |
| 5 |  | Wells Thompson | Wake Forest | M | 23 | 5'10 | 155 | Winston-Salem | NC | USA |
| Pick comment: Acquired from the Los Angeles Galaxy on Jan. 12, 2007, along with a conditional second round pick in 2008, in exchange for a portion of the Clint Dempsey replacement allocation. |
| 6 |  | Nico Colaluca | Virginia | M | 20 | 5'9 | 150 | Coventry | RI | USA |
| Pick comment: Acquired from the New York Red Bulls on April 21, 2006, along with Thiago Martins and a third round draft pick, in exchange for Jean Philippe Peguero. |
| 7 |  | John Cunliffe | Fort Lewis College | F | 22 | 5'11 | 160 | Edgworth, Bolton | | England |
| 8 | | Jerson Monteiro | Alabama - Birmingham | F | 21 | 6'0 | 170 | Houston | TX | USA |
| 9 |  | Anthony Wallace | South Florida, U20 National Team | D-M | 17 | 5'11 | 150 | St. Petersburg | FL | USA |
| 10 | | Andrew Boyens | New Mexico | D | 23 | 6'4 | 170 | Dunedin | | New Zealand |
| 11 |  | Bryan Arguez | West Kendall, U20 National Team | D-M | 17 | 6'2 | 165 | Miami | FL | USA |
| 12 | | Amaechi Igwe | Santa Clara, U20 National Team | D | 17 | 6'0 | 165 | Belmont | CA | USA |
| 13 |  | John Michael Hayden | Indiana | M | 22 | 5'10 | 160 | Louisville | KY | USA |
| Round 2 |
| Pick | Team
| Player | Affiliation | Position | Age | Ht | Wt | City | State | Country |
| 14 | | Abdus Ibrahim | U17 National Team | F | 15 | 6'1 | 165 | Richfield | MN | USA |
| Pick comment: Acquired from Toronto FC, along with Adrian Serioux, on Nov. 17, 2006 in exchange for Ronnie O'Brien. |
| 15 |  | Brad Evans | California - Irvine | F | 21 | 6'1 | 160 | Phoenix | AZ | USA |
| 16 |  | Robbie Findley | Oregon State | F | 22 | 5'9 | 165 | Phoenix | AZ | USA |
| Pick comment: Acquired from the Kansas City Wizards on December 15, 2006 in exchange for Kevin Hartman. |
| 17 | | Greg Dalby | Notre Dame | M | 21 | 6'0 | 174 | Poway | CA | USA |
| Pick comment: Acquired from Real Salt Lake on February 18, 2006 in exchange for the rights to Jordan Cila. |
| 18 | | Andrew Daniels | Brown | F | 21 | 6'2 | 175 | Milwaukee | WI | USA |
| Pick comment: Acquired from the Colorado Rapids on Jan. 12, 2007, along with a second round pick in 2008, in exchange for Greg Vanney and a third round pick in 2008. |
| 19 |  | Dane Richards | Clemson | F-M | 23 | 5'7 | 153 | Montego Bay | | Jamaica |
| 20 | | Josh Tudela | Indiana | M | 22 | 5'9 | 160 | Evansville | IN | USA |
| Pick comment: Acquired from Real Salt Lake (originally Chivas USA) on June 24, 2006 in exchange for the rights to Paul Broome. |
| 21 | | Nate Norman | Notre Dame | M | 21 | 6'1 | 170 | Rochester | MI | USA |
| 22 | | Ryan Guy | San Diego | F | 21 | 5'7 | 160 | Carsbad | CA | USA |
| 23 | | Ty Harden | Washington | D | 22 | 6'1 | 190 | Junction City | OR | USA |
| Pick comment: Acquired from the Los Angeles Galaxy on December 1, 2006 in exchange for the Colorado Rapids' 2006 natural second round selection (23rd) during the Joe Cannon trade. |
| 24 | | Brad North | Northwestern | F | 21 | 6'1 | 185 | The Woodlands | TX | USA |
| 25 | | Ryan Solle | Wake Forest | M | 21 | 5'8 | 160 | Broadway | NC | USA |
| 26 | | Corey Ashe | North Carolina | F-M | 20 | 5'6 | 140 | Virginia Beach | VA | USA |
| Round 3 |
| Pick | Team
| Player | Affiliation | Position | Age | Ht | Wt | City | State | Country |
| 27 | | Rich Asante | Syracuse | M | 22 | 5'4 | 160 | New York, Ontario | | Canada |
| 28 | | Scott Jones | North Carolina - Greensboro | M | 23 | 5'11 | 165 | Dallas | TX | USA |
| Pick comment: Acquired from the Columbus Crew on January 20, 2006 in exchange for FC Dallas' 2006 first overall fourth round pick (38th). |
| 29 | | Edson Elcock | Old Dominion | F-M | 22 | 5'7 | 145 | Brooklyn | NY | USA |
| 30 | | Steven Curfman | Wake Forest | M | 20 | 5'11 | 150 | Raleigh | NC | USA |
| 31 | | Omar Cummings | Cincinnati | F | 24 | 5'10 | 165 | Old Harbour | | Jamaica |
| Pick comment: Acquired from the Los Angeles Galaxy on April 7, 2006 by virtue of Cornell Glen playing in less than 16 games in the 2006 season. |
| 32 | | Jay Needham | Southern Methodist | M-D | 22 | 6'2 | 175 | Fort Worth | TX | USA |
| Pick comment: Acquired from the Colorado Rapids on December 14, 2006 in exchange for the rights for Brandon Prideaux, along with a 2008 natural third round pick. The 2007 pick was acquired by the Rapids from the New York Red Bulls on April 21, 2006, along with Thiago Martins and a first round draft pick in exchange for Jean Philippe Peguero. |
| 33 | | Sinisa Ubiparipovic | Akron | F-M | 23 | 5'9 | 155 | Mentor | OH | USA |
| Pick comment: Acquired from Chivas USA on November 21, 2006, along with a designated player slot, in exchange for Amado Guevara. |
| 34 | | Mike Banner | Southern Illinois | M | 22 | 5'10 | 160 | Washington, D.C | DC | USA |
| 35 | | Nick LaBrocca | Rutgers | M | 22 | 5'10 | 165 | Howell | NJ | USA |
| Pick comment: Acquired from FC Dallas on February 8, 2006 in exchange for the use of a Youth International slot in 2006. |
| 36 | | Justin Hughes | North Carolina | GK | 21 | 6'1 | 180 | Wake Forest | NC | USA |
| 37 | | Ricky Schramm | Georgetown | F | 21 | 5'11 | 170 | Eastchester | NY | USA |
| 38 | | Bryan Byrne | California - Santa Barbara | M | 24 | 5'8 | 155 | Castledermot | | Ireland |
| 39 | | Mike Sambursky | South Carolina | F | 22 | 5'10 | 180 | Houston | TX | USA |
| Round 4 |
| Pick | Team
| Player | Affiliation | Position | Age | Ht | Wt | City | State | Country |
| 40 | | Jeff Gonsalves | Rhode Island | F | 20 | 6'0 | 160 | Markham, Ontario | | Canada |
| 41 | | Aaron Chandler | San Francisco | F | 23 | 6'1 | 160 | Riverside | CA | USA |
| 42 | | Kurt Morsink | James Madison | F | 22 | 5'10 | 160 | San Jose | | Costa Rica |
| 43 | | Tommy Krizanovic | Jacksonville | F | 22 | 5'10 | 155 | Slavonski Brod | | Croatia |
| Pick comment: Acquired from Real Salt Lake on January 4, 2005 in exchange for the rights to Brian Dunseth. |
| 44 | | Tally Hall | San Diego State | GK | 21 | 6'4 | 205 | Gig Harbor | WA | USA |
| 45 | | Bobby Burling | Loyola Marymount | F | 22 | 6'5 | 195 | Monument | CO | USA |
| Pick comment: Acquired from the New York Red Bulls on August 17, 2006 in exchange for John Wolyniec. |
| 46 | | Cameron Dunn | California - Irvine | D | 22 | 5'10 | 150 | Alta Loma | CA | USA |
| 47 | | Simon Omekanda | Penn State | F | 22 | 5'8 | 175 | Rochester Hills | MI | USA |
| 48 | | Adam Cristman | Virginia | F | 22 | 6'0 | 180 | Glen Allen | VA | USA |
| Pick comment: Acquired from Real Salt Lake on Jan. 12, 2007 in exchange for the rights to Kyle Brown. Real Salt Lake acquired the pick from FC Dallas on Jan. 12, 2007 in exchange for a fourth round pick in 2008. |
| 49 | | Ben Hunter | North Carolina | F | 21 | 6'0 | 170 | Doncaster | | England |
| Pick comment: Acquired from the Colorado Rapids on January 18, 2006 by virtue of Chris Wingert starting less than 25 percent of the Rapids' games during the 2006 season. |
| 50 | | Luis Robles | Portland | GK | 22 | 6'1 | | Sierra Vista | AZ | USA |
| 51 | | Kyle Helton | Duke | D | 20 | 5'8 | 160 | Alpharetta | GA | USA |
| 52 | | Eric Ebert | California | M | 22 | 6'0 | 175 | Irvine | CA | USA |
