Just as a stream of genetically modified crops looked set to be approved for commercial production in the European Union, the approval procedure appears to have become bogged down once again by disagreements among and within member states. Old controversies have resurfaced in new forms. The intractability of the issues suggests that the regulatory procedure has had too narrow a focus, leaving outside its boundary many of the more fundamental aspects that cause people in the European Union most concern. Regulators have come under considerable pressure to ensure their risk assessment decisions are soundly science-based. Ethical issues have been deemed to lie beyond the scope of the regulatory procedure, as a matter to be considered separately by professional ethicists. Yet it has been suggested that all environmental controversies at root involve disputes about fundamental ethical principles. This paper examines how the ethical issues are currently suppressed or sidelined. It discusses how an appreciation of systems thinking and a check on the values that underpin decisions, using boundary testing questions, might contribute to a more constructive regulatory dialogue, with ethical issues considered as integral in a way that takes better account of people's concerns.