This article reports the recommendations of the Panel on Cost Effectiveness in Health and Medicine, sponsored by the US Public Health Service, on standardised methods for conducting cost-effectiveness analyses. Although not expressly directed at analyses of pharmaceutical agents, the Panel's recommendations are relevant to pharmacoeconomic studies. The Panel outlines a 'Reference Case' set of methodological practices to improve quality and comparability of analyses. Designed for studies that inform resource-allocation decisions, the Reference Case includes recommendations for study framing and scope, components of the numerator and denominator of cost-effectiveness ratios, discounting, handling uncertainty and reporting. The Reference Case analysis is conducted from the societal perspective, and includes all effects of interventions on resource use and health. Resource use includes 'time' resources, such as for caregiving or undergoing an intervention. The quality-adjusted life-year (QALY) is the common measure of health effect across Reference Case studies. Although the Panel does not endorse a measure for obtaining quality-of-life weights, several recommendations address the QALY. The Panel recommends a 3% discount rate for costs and health effects. Pharmacoeconomic studies have burgeoned in recent years. The Reference Case analysis will improve study quality and usability, and permit comparison of pharmaceuticals with other health interventions.