There is emerging interest in the use of discrete choice experiments as a means of quantifying the perceived balance between benefits and risks (quantitative benefit-risk assessment) of new healthcare interventions, such as medicines, under assessment by regulatory agencies. For stated preference data on benefit-risk assessment to be used in regulatory decision making, the methods to generate these data must be valid, reliable and capable of producing meaningful estimates understood by decision makers. Some reporting guidelines exist for discrete choice experiments, and for related methods such as conjoint analysis. However, existing guidelines focus on reporting standards, are general in focus and do not consider the requirements for using discrete choice experiments specifically for quantifying benefit-risk assessments in the context of regulatory decision making. This opinion piece outlines the current state of play in using discrete choice experiments for benefit-risk assessment and proposes key areas needing to be addressed to demonstrate that discrete choice experiments are an appropriate and valid stated preference elicitation method in this context. Methodological research is required to establish: how robust the results of discrete choice experiments are to formats and methods of risk communication; how information in the discrete choice experiment can be presented effectually to respondents; whose preferences should be elicited; the correct underlying utility function and analytical model; the impact of heterogeneity in preferences; and the generalisability of the results. We believe these methodological issues should be addressed, alongside developing a 'reference case', before agencies can safely and confidently use discrete choice experiments for quantitative benefit-risk assessment in the context of regulatory decision making for new medicines and healthcare products.