Bemidji State University has 13 National Titles: 7 NAIA, 1 NCAA D-III, 5 NCAA D-II
http://www.thebeaverpond.com/hockey_history.htm
University of Michigan, with 9 NCAA Championships. From: http://www.ncaa.org/library/records/ice_hockey/m_ice_hockey_champs_records
/2006/2006_d1_m_ice_hockey_champ_records.pdf
Montreal Canadiens with 24
UCLA - 100 Championships
Stanford with 540
Depends on which sport or sports you are asking about.
The University of Michigan Wolverines have the most Division I College Hockey Championships with 9. The closest to them is the University of North Dakota Fighting Sioux with 7.
116 national championships since 1895 in football. However most teams don't count their national championship pre ww2!
The UCLA Lady Bruins have won the most National Championships in Collegiate Fastpitch Softball...I believe they have won 25 or 26 National Championships.
MIT?
UCLA
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As of the 2007-08 season, the Michigan Wolverines have most the most NCAA championships in ice hockey with 9. 1948, 1951, 1952, 1953, 1955, 1956, 1964, 1996, and 1998. Denver and North Dakota are tied for second most with 7 each.
Princeton With 26 National Championships.