^#1: Chivas USA → MetroStars. 2006-01-20: MetroStars acquired this pick from Chivas USA in exchange for the #5 pick and defender Jason Hernandez.[ref 1]
^#5: MetroStars → Chivas USA. 2006-01-20: Chivas USA acquired this pick and defender Jason Hernandez from MetroStars in exchange for the #1 pick.[ref 1]
^#9: Colorado Rapids → Columbus Crew. 2005-01-14: Columbus acquired this pick from Colorado in exchange for forward Jeff Cunningham.[ref 2]
^#13: Chivas USA → New England Revolution → Columbus Crew. 2006-01-20: Columbus acquired this pick and a third-round selection in the 2007 MLS SuperDraft from New England in exchange for an allocation.[ref 3] New England had acquired this pick (originally a conditional pick) and the traded third-round 2007 selection from Chivas USA in exchange for salary considerations on 2005-09-10.[ref 4]
^#14: Real Salt Lake → Chicago Fire. 2005-01-03: Chicago acquired this pick and a third-round selection in the 2005 MLS SuperDraft from Real Salt Lake in exchange for defender Evan Whitfield and forward Dipsy Selolwane.[ref 5]
^#15: Columbus Crew → FC Dallas. 2005-04-26: FC Dallas acquired this pick and a youth international slot for the 2005 season from Columbus in exchange for forward Cornell Glen.[ref 6]
^#17: MetroStars → Real Salt Lake → MetroStars. 2005-02-01: MetroStars acquired this pick and an allocation from Real Salt Lake in exchange for defender Eddie Pope.[ref 7] MetroStars had the choice of swapping first-round selections in the 2005 MLS Supplemental Draft with Real Salt Lake or taking the highest RSL second-round 2006 SuperDraft selection. MetroStars chose the latter. Real Salt Lake had previously acquired this pick from MetroStars in exchange for use of a youth international slot for the 2005 season on 2005-01-14.[ref 8]
^#19: D.C. United → Chicago Fire → Kansas City Wizards. 2006-01-11: Kansas City acquired this pick and midfielder Will John from Chicago in exchange for midfielder Diego Gutiérrez.[ref 9] Chicago had acquired this pick from D.C. United in exchange for a third-round selection in the 2005 MLS SuperDraft on 2005-01-14.[ref 10]
^#20: Houston Dynamo → Chicago Fire. 2005-06-14: Chicago acquired this pick from San Jose in exchange for defender Kelly Gray.[ref 11] The San Jose franchise moved to Houston after the 2005 MLS season.
^#22: Chicago Fire → FC Dallas. 2005-01-14: FC Dallas acquired this pick and goalkeeper Henry Ring from Chicago in exchange for a third-round selection in the 2005 MLS SuperDraft.[ref 12]
^#25: Chivas USA → Los Angeles Galaxy. 2005-03-11: Los Angeles acquired this pick (originally a conditional pick) from Chivas USA in exchange for defender Ryan Suarez.[ref 13]
^#29: MetroStars → Kansas City Wizards. 2005-11-22: Kansas City acquired this pick from MetroStars in exchange for the rights to defender Taylor Graham.[ref 14]
^#33: Colorado Rapids → Columbus Crew. 2006-01-20: Columbus acquired this pick from Colorado in exchange for goalkeeper Matt Jordan.[ref 15]
^#38: Real Salt Lake → FC Dallas → Columbus Crew. 2006-01-20: Columbus acquired this pick from FC Dallas in exchange for a third-round selection in the 2007 MLS SuperDraft.[ref 16] FC Dallas had acquired this pick (originally one of two "future considerations") from Real Salt Lake in exchange for forward Jason Kreis on 2004-11-17.[ref 17][ref 18]
^#39: Columbus Crew → D.C. United. 2004-01-30: D.C. United acquired this pick, originally "future considerations", from Columbus in exchange for forward Devin Barclay.[ref 19][ref 15]
^#41: MetroStars → Houston Dynamo → MetroStars. 2006-01-20: MetroStars re-acquired this pick from Houston in exchange for goalkeeper Zach Wells.[ref 20] Houston (then San Jose) had acquired the pick from MetroStars in exchange for goalkeeper Jon Conway on 2005-12-05.[ref 21]
^#43: D.C. United → FC Dallas. 2004-07-23: FC Dallas acquired this pick and a second-round selection in the 2005 MLS Supplemental Draft (originally "future considerations") from D.C. United in exchange for forward Jason Thompson.[ref 22]
^#47: New England Revolution → D.C. United. 2005-01-20: D.C. United acquired this pick from New England in exchange for goalkeeper Doug Warren.[ref 23]