Many clinical decisions in urology involve uncertainty about the course of disease or the effectiveness of treatment. Many decisions also involve trade-offs; for example, an improvement in patient survival at the cost of an increased risk of treatment-related adverse effects. Decision analysis is a formal, quantitative method for systematically comparing the benefits and harms of alternative clinical strategies under circumstances of uncertainty. The basic steps in performing a decision analysis are to define the clinical scenario or problem, identify the clinical strategies to be considered in the decision, enumerate all of the important sequelae of each strategy and their associated probabilities, define the outcome of interest, and assign a value to each possible outcome. Health outcomes can be defined in a number of ways, including quality-adjusted survival. A key aspect of decision analysis is allowing the values of particular health outcomes to vary from patient to patient, depending on individual preferences. Decision analysis has already been used to assess a variety of prevention, screening and treatment decisions in urology, and there is much potential for its future application. Greater incorporation of decision-analytic techniques into urology research and clinical practice might improve decision making, and thereby improve patient outcomes.