BRAFO stands for Benefit-Risk Analysis for Foods. This European Commission funded project aims at developing a framework that allows quantitative comparison of human health risks and benefits of foods and food compounds based on a common scale of measurement.A methodology group brought together methodologies from several disciplines relevant to the evaluation of risks and benefits in food. This group reviewed and assembled the methodologies available. They produced this guidance document that describes a tiered ('stepwise') approach for performing a risk and benefit assessment of foods. This process starts with pre-assessment and problem formulation to set the scope of the assessment. This includes defining two scenarios, the reference and an alternative that are compared in the assessment. The approach consists of four tiers. In many cases, a lower tier assessment in which risks and benefits are qualitatively evaluated may be sufficient to show a clear difference between the health impacts of the two scenarios. In other cases, increasingly sophisticated methods to integrate risks and benefits quantitatively are used at higher tiers to assess the net health impact.