Lilley, who became president in November 2005, turned down an offer to complete his five-year contract, the Houston Chronicle reported.

Board Chairman Howard Batson acknowledged that Baylor made strides in a number of areas under Lilley's leadership. Fundraising hit record levels, Baylor moved up on U.S. News and World Report rankings and the SAT scores of new students went up.

"The reality is, the board lost confidence in John's ability to unite various Baylor constituencies," Batson said.

While Lilley was president, there were disputes about tenure and the style of the Baylor logo. Baylor, a Baptist institution, is also trying to become a major research university while maintaining its religious orientation.

"This is a time of transition as Baylor tries to become a top-tier university ... with a new emphasis on research in a setting that embraces both faith and learning," Batson said. "That is a time of change, and change is always hard."

Harold Cunningham, a regent, will be acting president until an interim is appointed.