In Europe, there seems to be widespread, morally based scepticism about the use of GMOs in food production. In response to this scepticism, the revised EU directive 2001/18/EC on the deliberate release into the environment of genetically modified organisms stresses the importance of respecting ethical principles recognized in the Member States. However, the directive fails to reflect the critical role of value judgements in scientific risk assessment and any subsequent approval procedure. In this paper we argue that it is important to make all ethically relevant assumptions involved in the approval procedure transparent and thus available for public scrutiny. Mapping the value judgements that are made in an environmental risk assessment and approval procedure, we describe the political liberal nature of the EU legislation. We then look more closely at the prescriptions for environmental risk assessment and approval of GMOs outlined in the directive. An environmental risk assessment views the world through a “risk window” that only makes visible that which has been predefined as a relevant risk. The importance of the value judgements that define the risk window consists in limiting the information the risk assessment can provide. In the penultimate section of the paper, the significance of the risk window is demonstrated through a case study of the approval of glyphosate resistant fodder beets (Beta vulgaris L. ssp. vulgaris) in Denmark.