Background Rare diseases are generally poorly understood from scientific and medical standpoints due, to their complexity and low prevalence. As a result, individuals living with rare diseases struggle to obtain timely diagnoses and suitable care. These clinical difficulties add to the physical and psychological impacts of living with chronic and often severe medical conditions. From the standpoint of pragmatist ethics, the morally problematic situations that adults living with rare diseases experience matter crucially. However, there is little known about these experiences.Methods (...) A survey study was conducted with 121 adults living with rare diseases in Québec, Canada, to identify morally problematic situations encountered in the healthcare system and everyday life as part of a participatory action research project. Morally problematic situations elicited internal tensions and constraints to agency.Results Adults living with rare diseases experienced morally problematic situations of stigmatization, disbelief, and sometimes abuse in the healthcare system. These situations were compounded by diagnostic delays, inadequate care, and suboptimal follow-up, and led some individuals to opt-out of medical care. In their personal lives, these individuals sometimes found themselves in situations of physical and financial dependency. They often also had to give up professional occupations, academic training, or life projects.Conclusions Adults living with rare diseases experience important morally problematic situations navigating the healthcare system and their everyday lives, some of which could be alleviated through interventions developed through future participatory action research. (shrink)