This article asserts that the normative, institutional and policy framework of an economy moulds the structure and performance of its innovation system. Three case studies of industry?higher education partnerships in South Africa's biotechnology sector challenge both the notion of a simple convergence within and between national innovation systems and the idea of an unproblematic adoption of 'best practice' at the organizational level. The contribution of industry?higher education partnerships to greater economic efficiency is shaped by the social conditions in which they are embedded. Rising levels of competition and new policy initiatives provide the fundamental impetus for collaboration and generate varying patterns of strategic alliances between governmental agencies, industry and higher education institutions.