The use of genetically modified organisms (GMOs) in agriculture and food production is the object of an intense and divisive debate. Drawing on a study on the public perception of agricultural gene technologies carried out in five European countries, the article deals with the policy aspects of the issue, and more precisely on the relation between institutions, experts and the public in a context of deep uncertainty. A theoretical framework is developed and compared with the study findings, suggesting that issues like the GMOs one represent a strong case for a more participatory policy-making. My conclusions suggest a style of governance based on the principles of deliberative democracy, as a suitable approach to the confrontation of different viewpoints and forms of knowledge. This appears to be the best way to improve the overall quality of policy-making: in this I include its legitimacy, the degree of public trust, and also the actual quality of its products. Strengthening the role of the public sphere seems more effective than simply increasing direct decision-making by the populace, and it offers an alternative to the 'elitist' solutions to the crisis of representative democracy.