The transformation of higher education systems under the pressure of new needs required by the "society of knowledge" in France and Italy has had a deep effect on the relationship between state and university, and therefore a direct impact on university governance. This article sums up the main results of a research carried out on university "Presidents" in France and "Rettori" in Italy, with the aim of understanding their views about the changing process in higher education systems and the related impact on their leading role. There emerges a picture of systems transiting from a traditional centralised Napoleonic structure to a new one where the growing autonomy requires a different kind of governance not previously experienced, and thus not easy to implement mostly because of the resistance coming from universities themselves. The majority of Presidents and Rectors seem aware of the changing process and the related problems even if they do not all agree upon feasible trends to follow. Such a disagreement appears to be an understandable consequence of the unstable and unpredictable direction of the changing situation in the two systems. (Contains 1 note.)