The university research environment has been undergoing profound change in recent decades. Aiming at international competitiveness and excellence, performance based university research funding systems have been implemented in many countries. However, evidence-based analysis of policy effects is scarce. This paper develops methods for evaluating the effect of university research policy on university system research output. We assume stable dynamics between inputs and outputs, and that effective policy change introduces external interventions and therefore structural changes into the system. We examine trends in input—HERD—and output—publications—at the national level over three decades and look for breaks signaling structural change.