Policy decisions on complex environmental risks often involve contested science. Typically there are no 'facts' that entail a unique correct policy. The evidence that is embodied in scientific policy advice requires quality assessment. Advice should be relevant to the policy issue, scientifically tenable and robust under societal scrutiny. In 2003, the Netherlands Environmental Assessment Agency adopted a standardized method, referred to as 'guidance', whereby key quality aspects of knowledge production and use are exhibited through a checklist for uncertainty assessment and communication. Although the guidance is not fully used within all projects yet, it is increasingly used, attitudes towards dealing with uncertainty in performing and reporting environmental assessments have changed, and communication on uncertainty in the agency's reports has improved over the past five years. In this letter, we present results from the application of the guidance to controversies on the risks of ambient particulate matter. The active deliberation on uncertainty in the policy–advisory setting brings about a joint learning process for advisors and policy makers, which leads to a deeper understanding and increased awareness of the phenomenon of uncertainty and its policy implications.