12 (The Big East had 3 in 2009)
ACC - 4
Big East - 3
Big10 - 2
Pac10 - 1
Big12 - 1
SEC - 1
2009 - Big East (Pitt, UConn, Louisville)
2006 - Big East (Villanova, UConn)
2005 - ACC (Duke, UNC)
2003 - Big12 (Oklahoma, Texas)
2002 - ACC (Maryland, Duke)
2001 - Big10 (Illinois, Michigan St)
2000 - Pac10 (Stanford, Arizona)
1998 - ACC (UNC, Duke)
1993 - Big10 (Indiana, Michigan)
1985 - Big East (Georgetown, St. John's)
1982 - ACC (UNC, UVA)
1980 - SEC (UK, LSU)
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This is not as uncommon as one might think and has occurred on more than one occasion in the NCAA men's Basketball tournament. As of 2013, the most recent such occurrence was in 2009 when not just two but three #1 seeds were from the same conference: Louisville (the #1 overall seed), Pittsburgh and Connecticut-- all from the late Big East Conference.
Since 1979, when the tournament started seeding teams, five #2 seeds have won the NCAA men's basketball tournament.