Background: A public policy publication in 2014 represented a first approach of the Brazilian Ministry of Health with the development of clinical guidelines for rare diseases. The process involved the engagement of several stakeholders and aimed at prioritising the main groups of anomalies for the beginning of the elaboration process. The lack of specific and validated methodology for the development of guidelines for rare diseases, as well as a lack of scientific evidence of high methodological quality are known barriers. However, in the process, other barriers were identified, even more impeding.

Objectives: To point out the barriers identified during the process of developing guidelines for rare diseases in Brazil.

Methods: Descriptive case study

Results: Rare diseases imply in not only fewer patients, but also fewer specialists in the topic and available therapies. Experts in diagnosis and care do not always have knowledge in health-technology assessment or evidence-based medicine. Another barrier relates to the exemption from conflict of interests of those involved, especially with the pharmaceutical industry. These factors imply difficulties, and even the impossibility of identifying specialists to compose the elaboration group. In addition, there is great resistance with the proposed method and the lack of commercial interest of pharmaceutical companies in producing or requesting authorisation from the regulatory agency to market important therapies, which represents an insurmountable barrier to guarantee access to the existing therapeutic options.

Conclusions: After two years of implementation of the Public Policy for Rare Diseases in Brazil, the prioritised guidelines are still under development. In this way, the identification of these barriers becomes an important process in the development of a specific methodology for developing guidelines for rare diseases and overcoming these challenges.