The small patient populations of rare diseases, the limited natural history of these conditions, and the lack of long-term experience with new treatments all contribute to the difficulty in determining the value of rare disease therapies. The issue can be further complicated by whether value is calculated in a single payer system, or a multi-payer system. Recently the Innovation and Value Initiative issued a report with the Everylife Foundation for Rare Diseases from a long-term project to bring together stakeholders to explore patient-centered outcomes across rare diseases to inform those discussions. We spoke to Rick Chapman, chief scientific officer of the Innovation and Value Initiative, about the challenges of assessing the value of rare disease therapies, the role qualitative data should play in value assessments, and the recommendations from the report.