Some aspects of the traditional process for the development of new potential therapeutics for rare disorders and the ensuing research on safety and efficacy are changing. This is due, in part, to the increased ability of families, parents, individuals with rare disorders, and advocacy organizations to access and control information, to provide monetary or other incentives, and to communicate directly with biopharmaceutical companies and clinical investigators. Increasingly, advocacy organizations (and by extension, the families they serve) create or participate in disorder registries intended to facilitate research by industry and access of families to clinical trials; fund promising bench and clinical research; and lobby for outcomes beneficial to drug developers and researchers, such as increased funding or facilitated FDA approval. The involvement of families in the research process is likely to have implications for how willing individuals are to participate in studies, their expectations and perceptions of the study experience, and their behavior during the study. Their increased level of involvement may also affect how families perceive and respond to a clinical trial in which the results are not as promising as hoped, as quickly as hoped. This partnership approach has implications for biopharmaceutical companies who sponsor treatment trials and for clinical investigators who lead and implement the trials. This qualitative interview study aims to describe, from the perspectives of parents of children involved in a clinical trial, research clinicians implementing the trial, and the company sponsoring the trial, the experience of this new, more collaborative research process. In this case, we will examine the Ataluren trial for Duchenne muscular dystrophy. The results from this study are hypothesis-generating for downstream research and can inform biopharmaceutical companies and clinician researchers as they plan and implement clinical trials for rare disorders and help guide advocacy groups and parent advocates as they partner with researchers and industry.