UCLA with 100 official NCAA Championships. I suspect they also lead with total national championships in sports like men's Rugby and volleyball, and women's Basketball before those sports offered official NCAA championships, but I'd like to know the total number. USC, when their favorite athletes aren't commiting double murders (not an official NCAA sport, but they're working on it), claims 107. My guess is UCLA has 115 or so at least.
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Miami men's tennis program winning 137 straight matches from 1957-1964.
Second place is Penn State womens volleyball with 109 wins.
As of September 17, 2012, the University of Michigan has 897 wins-the most by any College Football program, all-time.