The outbreak of bovine spongiform encephalopathy (hereinafter BSE) in Europe has brought about serious tensions and fears – not only among consumers, but also among the national and European authorities responsible for risk management. Faced with the incapacity of the existing system to control the situation, on the one hand, and the need to restore consumers’ confidence on the other, the EU and national regulators felt obliged to repair the weaknesses as soon as possible. However, remedial actions undertaken at the time of the BSE crisis were not always the product of thorough consultations and they were often not well coordinated. Thus, they became a source of disagreement among the various actors in play. The case Commission v. France, which I will examine more closely in this paper, illustrates such a conflict among the national and European scientific authorities. The judgment was delivered in 2001, but the problem of the successful integration of science into the regulatory decision-making process of the EU still remains unsettled. In this paper I will present suggestions as to how the situation could be influenced by the outcomes of recent reforms of European food safety law and the establishment of the European Food Safety Authority.