Current approaches to measuring innovation in higher education (HE) provide a very limited picture about the real scope of the innovation activities of higher education institutions (HEI) as they address only some dimensions of HEI innovativeness, which negatively affects the ability of the HEI to manage its innovative efforts. The purpose of this paper is to present a way forward on how to measure HEI innovation performance that will go further than the usual indices. It describes a five-perspective framework with dedicated, comprehensive metrics for the measurement of HEI innovation performance. To test the concept and the possibility of empirical application two consecutive surveys have been conducted. Survey of innovation performance was conducted in order to collect hard data on HEI innovation performance and 14 persons in charge of completing the innovation performance questionnaire were interviewed in order to better understand the availability and reliability of the requested data.