The European Union (EU) has repeatedly underlined the importance of higher education, research and innovation as drivers in the further development of Europe—economically, socially and culturally. One of the latest policy initiatives by the European Commission (EC) intended to promote this agenda is the European Universities Initiative (EUI) where alliances between universities across national borders are to identify new approaches for boosting European scientific cooperation. It might be argued that this development represents an attempt to find an organizational solution to the European policy ambitions in higher education, research and innovation. This article presents a framework for analysing European university alliances. Based on interviews with persons occupying key leadership and management roles in ten alliances, the article analyses the potential gains and perils alliances might face along four dimensions: their internal coordination, their ways of resolving conflicts, the commitment of member universities and the cultural characteristics of the alliances.