There are approximately 7,000 rare disorders, many of which are life-threatening. Diagnosis is often problematic, and therapies are few. Before the passage of the Orphan Drug Act in 1983, neither the pharmaceutical industry nor universities devoted much effort to research on rare diseases. Important changes have occurred within and outside universities that position them to play a significant role in developing orphan drugs. Several models are being employed to promote drug-related research, including disease-focused, discovery-focused, development-focused, and industry-partnership-focused approaches. However, significant barriers challenge universities' ability to fully contribute to orphan drug development. Academic institutions, along with industry, government, and not-for-profit organizations, must address these issues in order to advance the field. New initiatives designed to increase university-based orphan drug research include creating mechanisms to ensure program continuity, building research and regulatory support infrastructure, facilitating commercialization, expanding government support, and developing mutually beneficial partnerships among academe, industry, and government.