Which NCAA football team has won the most National Championships in modern football?

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For Division I - Football Bowl Subdivision (most commonly thought of as College Football around the nation).

Officially the NCAA does not officially name a National Champion for their Football Bowl Subdivision "FBS" (formerly known as Division I-A). They rely on outside organizations to name a National Champion. Currently that organization is the Bowl Championship Series. The teams with the most BCS National Titles are the University of Florida and Louisiana State University (LSU) with two. The BCS has been around for 11 years, so if that is what you would consider "modern era" that is your easy answer.

Other than that, really the only thing you can do is look at All Time National Championships. Before the BCS, there were a plethora of National polls and rankings, so there was no clear national champion every single year before 1998.

As for all time champions... Alabama claims the most all-time with 12. Notre Dame and Michigan both claim 11 and Ohio State, Oklahoma, Southern Cal all claim 7.

For National Collegiate Athletic Association Divisions not including Division I - FBS (most of which are not commonly considered as college football on the same level as Division I - FBS).

The question is which team has won the most national championships. (And though not clearly stated, I'm assuming the questioner intended the answer to be limited to FBS, aka, Divsion I-A, teams. If not, the answer is the Division III Mount Union Purple Raiders, with 10.

Although the National Collegiate Athletic Association (NCAA) does not officially award a national championship in Division I FBS, it does recognize a number of polling and ranking organizations that name a national champion and recognize a members right to claim a national championship by being selected by one of these organizations. A complete list of every national championship recognized by the NCAA can be found at the link below from 1869 through 2006. The eight schools with the most national championships recognized by the NCAA are listed below.

Princeton - 28
Yale - 27
Notre Dame - 21
Alabama - 17
Southern California - 17
Oklahoma - 16
Michigan - 15
Ohio State - 14
List of NCAA recognized national championships:
http://www.ncaa.org/champadmin/ia_football_past_champs.html

It should be noted though, that while a school may be recognized for a certain number of national championships by the NCAA, that does not necessarily mean the school claims all of the championships.
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