Rigorously testing the growing medication pipeline for rare conditions continues to be an industry challenge. The low prevalence rates for rare diseases run contrary to the phased drug development processes that are the standard and poses significant obstacles for developing, testing, and approval of promising treatments. The intent of this position paper is to bring together into a practical framework three elements of clinical research (N-of-1, adaptive design techniques, and multiple baseline) for testing small and variable samples of patients undergoing treatment. The objective is to bring continuity and best practices to the evaluation of pharmaceutical products for treating rare disease. Specifically, the paper discusses general principles for when and how they should be applied and what limitations should be considered when developing methods for testing treatments for rare diseases.