| Round 1 |
| Pick | Team
| Player | Affiliation | Position | Age | Ht | Wt | City | State | Country |
| 1 |  | Jarrod Smith | West Virginia | F | 22 | 6'1 | 180 | Havelock North | | New Zealand |
| 2 |  | Desmond Brooks | Saint Mary's | D | 21 | 6'0 | | Fresno | CA | USA |
| Pick comment: Acquired from Real Salt Lake. The pick originally belonged to the Columbus Crew. |
| 3 |  | Aaron Hohlbein | Wisconsin | M-D | 21 | 6'0 | 170 | Middleton | WI | USA |
| 4 |  | John DiRaimondo | St. Louis | M | 20 | 5'7 | 155 | St. Louis | MO | USA |
| Pick comment: Acquired from Real Salt Lake. |
| 5 |  | Steve Purdy | California | D | 21 | 6'4 | 190 | San Jose | CA | USA |
| 6 |  | Randi Patterson | North Carolina - Greensboro | F | 21 | 5'9 | 170 | Hackensack | NJ | USA |
| 7 |  | Nick Noble | West Virginia | GK | 22 | 6'4 | 200 | Damascus | MD | USA |
| Pick comment: Acquired from Chivas USA. |
| 8 | | Mark Totten | James Madison | M | 22 | 6'1 | 170 | Chalfont | PA | USA |
| 9 |  | Sandi Gbandi | Alabama - Birmingham | M | 23 | 5'10 | 155 | Houston | TX | USA |
| 10 | | Gordon Kljestan | Seton Hall | D | 23 | 6'0 | 170 | Huntington Beach | CA | USA |
| Pick comment: Acquired from the Colorado Rapids. |
| 11 |  | Shawn Crowe | Florida International | GK | 22 | 6'3 | 195 | Aurora | CO | USA |
| 12 |  | Phil Marfuggi | Clemson | GK | 20 | 6'0 | 198 | Manalapan | NJ | USA |
| 13 |  | Nick Hatzke | California - Berkeley | M | 23 | 5'9 | 155 | San Jose | CA | USA |
| Round 2 |
| Pick | Team
| Player | Affiliation | Position | Age | Ht | Wt | City | State | Country |
| 14 | | Daryl Roberts | Liberty | F | 23 | 6'1 | 170 | Trincity | | Trinidad |
| 15 |  | Ryan Junge | Creighton | D | 22 | 6'1 | | Omaha | NE | USA |
| 16 | | Michael Todd | Hofstra | F | 24 | 6'0 | 182 | Cleveland | | England |
| 17 |  | Haddon Kirk | North Carolina State | D | 23 | 6'4 | 199 | Winston-Salem | NC | USA |
| 18 | | Kevin Long | San Francisco | D | | 6'3 | 170 | Irvine | CA | USA |
| 19 | | Sal Cacavale | American | M | 21 | 5'7 | 145 | West Islip | NY | USA |
| 20 | | Erasmo Solorzano | California - Riverside | M | 21 | 5'8 | 160 | Riverside | CA | USA |
| 21 | | Osei Telesford | Liberty | D | 23 | 5'10 | 160 | San Juan | | Trinidad |
| 22 | | Zach Kirby | Boston | D | 22 | 6'1 | 175 | Marietta | GA | USA |
| Pick comment: Acquired from FC Dallas. |
| 23 | | Tonci Skroce | Illinois - Chicago | M | 22 | 6'1 | 177 | Zadar | | Croatia |
| Pick comment: Acquired from the Colorado Rapids. |
| 24 | | Raul Batista | San Diego State | M | 22 | 6'1 | 185 | Salida | CA | USA |
| Pick comment: Acquired from D.C. United. |
| 25 | | Gary Flood | Hofstra | D | 21 | 5'10 | 160 | Hauppauge | NY | USA |
| 26 | | Taylor Canel | California State - Northridge | M-F | | 5'10 | 167 | Sherman Oaks | CA | USA |
| Pick comment: Acquired from the Columbus Crew. The pick originally belonged to Houston. |
| Round 3 |
| Pick | Team
| Player | Affiliation | Position | Age | Ht | Wt | City | State | Country |
| 27 | | Hunter West | South Florida | F | 23 | 5'11 | 170 | Bradenton | FL | USA |
| 28 | | Jared Kent | Old Dominion | M | 24 | 5'8 | 145 | Marietta | GA | USA |
| Pick comment: Acquired from the Columbus Crew. |
| 29 | | Chris Konopka | Providence | GK | 21 | 6'5 | 215 | Toms River | NJ | USA |
| 30 | | Eric Frimpong | California - Santa Barbara | M | 21 | 5'6 | 140 | Sunyani | | Ghana |
| Pick comment: Acquired from Real Salt Lake. |
| 31 | | Anthony Hamilton | California - Irvine | F | 21 | 6'0 | 160 | Grand Terrace | CA | USA |
| Pick comment: Acquired from the Los Angeles Galaxy. |
| 32 | | A.J. Godbolt | Maryland | M | 22 | 5'10 | 175 | Austin | TX | USA |
| Pick comment: Acquired from the New York Red Bulls. |
| 33 | | Lyle Martin | California State - Bakersfield | F | 21 | 6'0 | | Bakersfield | CA | USA |
| 34 | | Asmir Pervan | Saint Leo | F | 23 | 6'2 | 175 | Simmern | | Germany |
| 35 | | Kosuke Kimura | Western Illinois | M | 22 | 5'8 | 155 | Kanagawa | | Japan |
| Pick comment: Acquired from FC Dallas. |
| 36 | | Riley O'Neill | Kentucky | F | 21 | 6'2 | | Cambell River, British Columbia | | Canada |
| 37 | | Guy-Roland Kpene | Dowling College | F | 23 | 5'10 | | Abidjan | | Ivory Coast |
| 38 | | Chris Loftus | Duke | F | 22 | 6'5 | 195 | Springfield | IL | USA |
| 39 | | Erik Ustruck | Santa Clara | F | 22 | 5'9 | 163 | St. Louis | MO | USA |
| Round 4 |
| Pick | Team
| Player | Affiliation | Position | Age | Ht | Wt | City | State | Country |
| 40 | | Tyler Hemming | Hartwick College | M | 21 | 6'0 | 175 | London, Ontario | | Canada |
| 41 | | Ted Niziolek | Seton Hall | M | 21 | 5'11 | 160 | Clifton | NJ | USA |
| 42 | | Justin Douglass | Missouri State | D | 21 | 6'0 | 175 | Spring | TX | USA |
| Pick comment: Acquired from the Kansas City Wizards. |
| 43 | | Kyle Reynish | California - Santa Barbara | GK | 23 | 6'3 | 200 | Valencia | CA | USA |
| 44 | | Kiel McClung | UCLA | D | 21 | 6'1 | 180 | Palmdale | CA | USA |
| 45 | | Chase Wileman | Southern Methodist | M | 20 | 5'7 | 135 | Grand Prairie | TX | USA |
| Pick comment: Acquired from the New York Red Bulls. |
| 46 | | Danny Cepero | Pennsylvania | GK | 21 | 6'2 | | Baldwin | NY | USA |
| Pick comment: Acquired from Chivas USA. |
| 47 | | Daniel Woolard | Midwestern State | D | 22 | 5'10 | 155 | Bedford | TX | USA |
| 48 | | Michael Kraus | Creighton | M-F | 22 | 5'9 | | Memphis | TN | USA |
| Pick comment: Acquired from FC Dallas. |
| 49 | | Dustin Kirby | Ohio State | D | 22 | 5'10 | 170 | Mentor | OH | USA |
| Pick comment: Acquired from the Colorado Rapids. |
| 50 | | Kevin Burns | Connecticut | M | 21 | 6'1 | 175 | Greenfield | IN | USA |
| Pick comment: Acquired from D.C. United. |
| 51 | | | | | | | | | | |
| Pick comment: The New England Revolution did not make a pick. |
| 52 | | Willy Guadarrama | Campbell | F | 22 | 5'10 | 170 | Cedar Park | TX | USA |
| Pick comment: Acquired from Houston Dynamo. |
