As of 2012, the Pac 10 has the most NCAA Division I national championships in Basketball with 15 total championships. UCLA, the winningest team in College Basketball, won 11 of those.
Here is the championship count for the other main conferences:
This is using only teams current conferences, as going back and finding the each team's conference at the time of the championship would be too much. However had I done this the Pacific 10 would still be on top as Arizona's championship and UCLA's 11 championships were won while playing in the AAWU/Pac-8/Pac-10, all of which were name changes of the same conference. Oregon and California won their national championships while playing in the PCC. The Pac-10 is generally considered to be the successor to the PCC although they are not the same organization.
SEC
big ten
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PAC 10
SEC
I think its the SEC(South Eastern Conference)
Pac-10 just earned it's 400th maintaining it's place atop the list
SEC
UCLA holds the record for the most NCAA Men's Division
The UCLA Lady Bruins have won the most National Championships in Collegiate Fastpitch Softball...I believe they have won 25 or 26 National Championships.
40 national championships, 38 ncaa national championships
They have won 21 national wrestling championships