Once an external factor has been deemed likely to influence human health and a dose response function is available, an assessment of its health impact or that of policies aimed at influencing this and possibly other factors in a specific population can be obtained through a quantitative risk assessment, or health impact assessment (HIA) study. The health impact is usually expressed as a number of disease cases or disability-adjusted life-years (DALYs) attributable to or expected from the exposure or policy. We review the methodology of quantitative risk assessment studies based on human data. The main steps of such studies include definition of counterfactual scenarios related to the exposure or policy, exposure(s) assessment, quantification of risks (usually relying on literature-based dose response functions), possibly economic assessment, followed by uncertainty analyses. We discuss issues and make recommendations relative to the accuracy and geographic scale at which factors are assessed, which can strongly influence the study results. If several factors are considered simultaneously, then correlation, mutual influences and possibly synergy between them should be taken into account. Gaps or issues in the methodology of quantitative risk assessment studies include 1) proposing a formal approach to the quantitative handling of the level of evidence regarding each exposure-health pair (essential to consider emerging factors); 2) contrasting risk assessment based on human dose–response functions with that relying on toxicological data; 3) clarification of terminology of health impact assessment and human-based risk assessment studies, which are actually very similar, and 4) other technical issues related to the simultaneous consideration of several factors, in particular when they are causally linked.