The ramifications of the BSE crisis of the 1990s have stretched far into the 21st century. The collapse of consumer confidence caused by shortcomings in the institutionalisation of scientific knowledge within both the EU Member States and within the Union itself prompted wholesale re-evaluation of the prevailing structures of science-based decision making. However, the loss in consumer confidence was not the only catalyst for the change in the manner in which we view the legitimate use of science within government. In addition to the undeniable need for a review of the quality of scientific advice used to verify agricultural production methods, the extraordinary degree of public political disquiet about the authorised use of genetically modified organisms within agriculture and industry has raised new questions about science-based governance. Today, the issue is not merely one of assuring that the science used in governance is sound. Instead, thought must also be given to the balancing of scientific opinion against wider ethical and social values.