Public and stakeholder participation in decision-making has become ‘common jargon’, driven by recent legislation and international agreements. Substantial experience now exists, largely based on specific, often local, initiatives. However, many fundamental aspects remain inadequately addressed or problematic. Definitions of participation tend to be all-encompassing and conceptual premises are often side-lined. Also, how to scale up these processes and treat their outcomes at the national and international level within the boundaries of current legislation is unclear. The example of the commercialisation of agricultural genetically modified organisms in Europe is used here to explore which participatory processes have been used and the issues they raise in terms of environmental governance, the implications for institutional change, and the type and role of science in decision-making.