USL First Division Qualifying
 All eight U.S.-based teams in the USL First Division will participate in the 2006 U.S. Open Cup. This year, expansion side Miami FC will enter the tournament in the second round along with the three teams that finished the lowest in the 2005 regular season. The remaining four clubs in the USL-1 begin play in round three.
Second Round entries: Minnesota Thunder, Miami FC, Virginia Beach Mariners, Charleston Battery.
Third Round entries: Atlanta Silverbacks, Rochester Raging Rhinos, Seattle Sounders, Portland Timbers.
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