Globally, an estimated 350 million people are affected by a rare disease diagnosis. Knowledge limitations persist for the majority of rare conditions due to systemic and structural challenges in healthcare and research. Disease-specific patient populations are often small and geographically dispersed; funding support for research is restricted; and diagnostic delays are common due to disease complexities, limited medical training for practitioners, and evolving foundational knowledge related to disease characterization. Patient registries can be effective, convenient, and cost-efficient tools to support documentation of the natural history of a disease, centering patients as research partners in the process while uniting rare communities around a common initiative. Current global trends towards innovative and patient-centered healthcare are enabling patient registries to increasingly emerge as valuable tools for use within rare disease research and drug development. This article describes the value of and rationale for establishing rare disease patient registries and the considerations and challenges that stakeholders, such as researchers, industry, health care providers, and patient community organizations, may encounter.