Rare disease clinical trials (CTs) pose challenges to regulators and researchers alike. Their designs are complicated due to the small number of patients, the incomplete understanding of the natural history of a rare disease and the heterogeneity of patients, among other reasons. Patient Reported Outcomes (PROs) are important CTs endpoints because they reflect how patients feel and survive. However, using PROs as endpoints further adds to the complexity of rare disease trials. In this study, with a focus on rare diseases-specific products, we reviewed the biological application licenses approved by the Center for Biologics (CBER) from 1998-2016. We aimed to identify how PROs have been used in rare-diseases-specific products compared to other products regulated by CBER, e.g. vaccines which represent large CTs. We explore the study designs, types of endpoints (primary, secondary) and the statistical techniques used. During 1996-2016, CBER approved 40 vaccines and 80 products associated with CTs, 17.5% (14/80) products used PROs and were indicated for rare diseases. We compare the use of PROs in such products and present the common challenges for data collection and analysis.