John D. Wiley, chancellor of the University of Wisconsin at Madison since 2001, announced today that he would step down in September 2008. He said now was the time to begin a transition, as the university will be up for its 10-year reaccreditation next year and will also be in the middle of the state’s biennial budget cycle.

Mr. Wiley, 65, and other university leaders have clashed with Republican state lawmakers in recent years, and the Wisconsin State Journal today called the chancellor’s job a “hot seat.” The sticking points between the university and its neighbors in the nearby Wisconsin Capitol have included budget issues, stem-cell research, and an admissions policy that considers race and ethnicity.

However, Wisconsin’s Democratic governor, Jim Doyle, said Mr. Wiley’s legacy is a “world-leading research institution that drives our economic growth.”

Mr. Wiley acknowledged that the university faced difficult budget years during his tenure. “It’s been a period of cut after cut,” he said in a written statement. “To the extent that we were able to do that with minimal adverse effect on academic programs, I’m very proud of that.”

After first arriving on the Madison campus as a graduate student in physics in 1964, Mr. Wiley spent 30 years at the university as a faculty member and administrator, including stints as provost and dean of the graduate school. He says he will return to the faculty. —Paul Fain