Mangino's resignation came after the school completed an internal review into his treatment of players who complained about the alleged abuse.
He denied the allegations.
Mangino, the national Coach of the Year in 2007, finishes his KU career with a disappointing 5-7 2009 season (1-7 Big 12 Conference).
Assistants David Beaty, Clint Bowen and Bill Miller will share interim head-coaching duties until a permanent replacement is hired by Athletic Director Lew Perkins.
"We appreciate the eight years Mark has given to rebuilding our football program," Perkins said.
Perkins said legal counsel told him he cannot release documents related to the investigation or details about the settlement agreement between Mangino and the school.
Mangino, who led the team to a bowl game in four of his last seven seasons, had a 50-48 record at Kansas, two wins shy of the 52-win record set by A.R. Kennedy in 1910.
In 2008, Mangino signed a contract extension through 2012 that increased his annual salary to $2.3 million.
Copyright 2009 by United Press International.
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