This article discusses how Centres of Excellence (CoE) and the existence of several logics in these centres can contribute to the differentiation of the strategic profiles of universities. The study sees research centres as a way to organize research activities in Higher Education Institutions (HEIs) in order to target both excellence but also societal challenges through focused thematic research. It reveals how societal challenges and their interpretation by these centres contribute to the differentiation of the strategic profiles of universities. Studies of centres of excellence programs in Sweden and Japan reveal differences in how their mission is formulated for relevance and excellence. The results indicate that contrasting missions of HEIs are accommodated through the dual logics of these centres relating both to autonomy and industry collaboration. The study shows that long-term funding gives these centres flexibility to set the agenda and focus on their strategic core activities. In other words, a logic of autonomy guides their strategic choices of research activities over the long-run as well as collaborators. Nevertheless, these centres are also developing strategies to cope with dilemmas stemming from the excellence-relevance and evaluation templates that emerge in the nexus of their collaborative ties with industry, government and universities.