In this article, I endeavour to examine concrete challenges that arise with regard to implementation of the precautionary principle in the field of European Union regulation of genetically modified organisms (GMOs). Developed by the European courts into a general legal principle, precaution requires EU regulators to strike a balance between scientific and political legitimacy when taking decisions on risk-entailing products. Following this understanding, the current GMO legislation creates precautionary governance structures that allow for a broad input into the authorisation process, not only of scientific, but also of 'other legitimate factors'. At the same time, it can be criticised for narrowly defining precaution as a decision rule, which, if applied correctly, will lead the decision maker to the 'right' decision. I argue that this misconception is one of the reasons why, in the current authorisation practice, the EU institutions fail to apply the principle in a balanced way, falling into the extremes of either purely science-based decision making or a highly politicised precautionary rhetoric. I suggest that in order not to be paralysing, precaution should be understood as a procedural principle that provides for precautionary governance, thus enabling regulators to make appropriate risk choices.