Background: While randomized controlled trials represent the highest level of evidence we can generate in comparative effectiveness research, there are clinical scenarios where this type of study design is not feasible. The Comparative Effectiveness Analyses of Surgery and Radiation in localized prostate cancer (CEASAR) study is an observational study designed to compare the effectiveness and harms of different treatments for localized prostate cancer, a clinical scenario in which randomized controlled trials have been difficult to execute and, when completed, have been difficult to generalize to the population at large. Methods: CEASAR employs a population-based, prospective cohort study design, using tumor registries as cohort inception tools. The primary outcome is quality of life after treatment, measured by validated instruments. Risk adjustment is facilitated by capture of traditional and nontraditional confounders before treatment and by propensity score analysis. Results: We have accrued a diverse, representative cohort of 3691 men in the USA with clinically localized prostate cancer. Half of the men invited to participate enrolled, and 86% of patients who enrolled have completed the 6-month survey. Conclusion: Challenging comparative effectiveness research questions can be addressed using well-designed observational studies. The CEASAR study provides an opportunity to determine what treatments work best, for which patients, and in whose hands.