Rare diseases are an important part of the public health, affecting 6-8% of the population, and drugs intended for rare diseases comprise the fastest growing subcategory of new drug approvals in the United States. However, clinical study of therapeutics in these populations is limited by the low prevalence of these diseases, and the natural history or pathogenesis of the disease may be poorly described. In addition, commonly used strategies for evaluation of postapproval safety and effectiveness, such as meta-analyses and review of spontaneous adverse event reports, may not be applicable. Alternative methodological approaches, including natural history studies, adaptive clinical trial designs, and epidemiological studies using patient-organized registries, show substantial promise for the study of rare disease therapeutics. Bayesian trials and distributed networks of large electronic databases are the most promising strategies for active and prospective monitoring of clinical interventions for rare diseases.