Europe’s pharmaceutical industry is generally presented by the European Commission as both a success and a reason for hope during the current hard times. Indeed, whereas the latter have often been interpreted within the member states as a pretext for cutting health budgets, and thus the prices or reimbursement rates of medicines, the Commission’s pharmaceutical unit (once in DG Enterprise, now in DG SANCO) has successfully sought to maintain the privileged status of pharmaceutical companies who produce ‘original’ drugs. However, since 2008 in particular, this Commission support has come under increasing pressure from actors in DG ECFIN, DG Competition and from within DG SANCO itself. This paper will explain these intra-Commission tensions using on the one hand an analytical framework grounded in constructivism, institutionalism and political sociology and, on the other, interview, documentary and bibliometrical data. The overall claim made in this paper is that despite the deep criticisms made from within of existing Commission policy on pharmaceuticals, its instruments and legitimacy have nevertheless been reproduced by mobilizing a logic of action based on ‘innovation’ that has yet to be fundamentally problematized and questioned.