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The purpose of this study is to establish a new performance measurement method for academic actors for their changing roles in innovation systems. The widely accepted triple helix and systems of innovation models show changing and overlapping roles of academic, industrial and governmental actors. In previous innovation systems, universities were not focused on applied research and technology transfer as much as they are now. Current literature shows a changing role of universities and importance of their involvement in innovation systems.Although academic organizations' roles have changed in innovation systems, academic performance measurement systems (APMS) are not adapted to examine innovation related performance factors. Many APMS focus on key performance indicators (KPIs) such as; publications, research projects and patents. However, the new APMS needs to assess the activities and processes that are related to innovation, such as; technology transfer processes, collaborative innovation activities, consultancies and academic spinoffs.For this study a new APMS is applied according to the needs of universities by using a synthetic data based on an engineering department's KPIs. APMS scores are calculated based on the cumulative metric of all research and innovation activities and, weighted according to the needs and considerations of the university. The results of this study show that many of those academicians who have great performance in publications and academic research do not necessarily have high-level performance in innovative activities. In fact the results show that those who had high points in some measurements have very low performance in others. For the management point of view, it may be more effective to position academicians for different roles and assess their performance accordingly as innovation-targeted, teaching-targeted and research-targeted academicians.