The 2006 season was the 94th year of competitive soccer in the United States.

The home team or the team that is designated as the home team is listed in the left column; the away team is in the right column.

Win Draw Loss Purple indicates Supporters' Shield clinched Yellow indicates Regular Season Runners-up clinched Green indicates playoff berth clinched Commissioner's Cup, bye to semifinal round of playoffs Bye to semifinal round of playoffs First round of playoffs Quarterfinals and Semifinals 2-game aggregate Higher seeded team hosted first game Purple indicates regular season champion Green indicates playoff berth clinched 1New Hampshire was penalized 1 point for use of an ineligible player in a game.

Home teams listed on top of bracket