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Baylor University's board of regents fired the Baptist school's president on Thursday, saying they had lost confidence in his ability to "unite various Baylor constituencies."

John M. Lilley, on the job less than three years, rejected an offer to serve out his five-year contract as regents searched for a replacement.

Lilley's relatively brief tenure was marked by disputes over tenure and even over the university's logo. But how best to achieve Baylor's goal of becoming a major research university without sacrificing its strong Christian character appears to have been an issue, as well.

Board Chairman Howard K. Batson, speaking to reporters in a conference call, declined to say exactly why regents replaced Lilley, who was hired in November 2005. Lilley's time in office coincided with record fund-raising, higher SAT scores for incoming students and a jump in the school's ranking on a list compiled by U.S. News and World Report, Batson acknowledged.

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

"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. That is a time of change, and change is always hard."

Regent Harold Cunningham will serve as acting president until an interim president can be found.

Batson said regents offered to let Lilley to remain in office while they conducted a national search for his replacement. Lilley declined.

In an e-mail to the Baptist Standard, he appeared defiant. "I deeply regret the action of the board, and I do not believe that it reflects the best interests of Baylor University," he wrote.

A key issue has been Baylor's Vision 2012, an ambitious plan that calls for the school, the world's largest Baptist university, to marry strong Biblical principles with cutting-edge research.

Batson said that Lilley's faith was never an issue — Lilley is Baptist, but had been active in the Presbyterian church before he was hired for the top spot at Baylor — but noted that the next president will be Baptist.

Jeff Reeter, managing partner at Texas Financial Group in Houston and former chairman of the Baylor Development Council, said the concern is not that Lilley has taken Baylor in a more secular direction, but that the school is ready for an even "bolder" vision.

"Baylor has a unique position in our world that many in academia thinks is a difficult position," he said, noting the often-mentioned conflict between Biblical beliefs, including creationism or intelligent design, and science. "We feel that is part of our calling. I think Baylor believes the two things cannot only coexist, but they can powerfully coexist."

jeannie.kever@chron.com