In order for research programs at academic medical centers and universities to survive and thrive in the increasingly challenging economic, political and regulatory environment, successful transformation is extremely important. Transformation and quality management techniques are increasingly well established in medical practice organizations. In medical research organizations, the introduction of quality management systems is a more recent development. Mayo Clinic has now completed five years of implementing quality management systems in support of its national research organization. This article describes the quality management system under development within research at Mayo Clinic, key action steps taken in transforming the research management systems, results achieved to date in improving performance, and lessons learned. (Contains 3 figures.)