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.
Miami men's tennis program winning 137 straight matches from 1957-1964.
Second place is Penn State womens volleyball with 109 wins.
UCLA they have 101 national championships in all sports. (11 in basketball)
University of Georgia
Stanford with 540
Depends on which sport or sports you are asking about.
The Texas Longhorns
Kentucky 1st= 1900Wins+ UNC 2nd= 1900Wins+ ?
The New York Yankees have the most championships in any sports history. They have a total of 26 championships and have appeared in the championship 39 times.
For the category of Division I sports in the men's and women's field, the university that has the most NCAA championships is UCLA. They have 109 as of 2012. Stanford is next with 103, followed by USC with 96.
UCLA - 100 Championships