The purpose of this study was to describe and analyse leadership challenges in the organisation of strategic research centres, focusing on the relationship between organisation and the level of institutionalisation. Four main themes of leadership challenges were identified: (1) the "changing university context," including relationships with top management and faculties; (2) "research strategy," considering decisions about diversity or a focused perspective; (3) "management," dealing with prioritising administrative work; (4) "affiliation," the sense of belonging to a strategic research centre, comprising issues of leadership, trust, attitude towards recruitment and succession. We concluded that leadership and effective administration are vital for research collaboration, not only within small research groups as been shown in other studies, but also within large groups in university-based research centres.