^#7: D.C. United → Houston 1836. 27 May 2005: Houston 1836, at the time still based in San Jose as the Earthquakes, acquired this first-round selection from D.C. United in exchange for the #1 draft slot in the MLS waiver rankings. The clubs also agreed to switch waiver slots for the remainder of the 2005 Major League Soccer season. D.C. immediately used the #1 slot to sign defender John Wilson.[ref 1]
^#8: Houston 1836 → FC Dallas. 25 March 2005: FC Dallas acquired this first-round selection from Houston 1836, at the time still based in San Jose as the Earthquakes, in exchange for forward Julian Nash.[ref 2]
^#31: D.C. United → MetroStars. 4 February 2005: MetroStars acquired this third-round pick, originally "future considerations", from D.C. United in exchange for midfielder Kenny Arena.[ref 3]
^#37: Chivas USA → Houston 1836. 24 March 2005: Houston 1836, at the time still based in San Jose as the Earthquakes, acquired this fourth-round pick from Chivas USA in exchange for defender Victor Arbelaez.[ref 4]
^#38: Real Salt Lake → Colorado Rapids. 20 April 2005: Colorado Rapids acquired this fourth-round selection from Real Salt Lake in exchange for midfielder Seth Trembly.[ref 5]
^#39: Columbus Crew → MetroStars → FC Dallas. 5 August 2005: FC Dallas acquired this fourth-round pick, originally a conditional selection, from MetroStars in exchange for midfielder Eric Quill.[ref 6] On 1 July 2005, MetroStars had acquired this fourth-round pick from Columbus Crew in exchange for goalkeeper Jonny Walker.[ref 7]
^#41: MetroStars → Real Salt Lake. 25 January 2006: Real Salt Lake acquired this fourth-round selection from MetroStars in exchange for forward Jordan Cila.[ref 8]
^#42: FC Dallas → Colorado Rapids → Chicago Fire. 15 September 2005: Chicago Fire acquired this fourth-round pick from Colorado Rapids in exchange for midfielder Alexandre Boucicaut.[ref 9] On 29 June 2005, Colorado had acquired this fourth-round pick from FC Dallas in exchange for midfielder John Pulido.[ref 10]
'^#45: Pick originally belonged to Colorado Rapids. → Kansas City Wizards.