Higher education institutions are in a period of profound transformation. In particular, many governments have implemented mechanisms that attempt to relate funding to performance. In this article, we reflect about the relevance of those changes from a regional point of view, by analysing the recent introduction of a performance-based research funding system in Italy. The findings lead to policy indications, questioning the effectiveness of selective funding of universities based on national research assessment exercises when there is heterogeneity across regions in universities scientific performance and, at the same time, there is a huge dispersion of research performance within the individual universities.