Background: Systematic approaches to involving patients and clinicians in setting agendas have been led by the Cochrane Collaboration and reported in wider research programmes for over ten years. More recently the James Lind Alliance has supported working partnerships of patients and clinicians to identify the most important gaps in knowledge about the effects of treatments. This paper scopes the research literature addressing such efforts. Methods: Electronic searches of bibliographic databases were complemented by handsearching and contacting key authors. Two researchers, initially working independently, included and described the relevant reports. Results: Over 250 studies addressed patients’ or clinicians’ priorities for research and outcomes for assessment. This literature described different routes for patients and clinicians to contribute to research agendas, engaging directly (148) or indirectly with research, in order to identify important areas for research, questions for research and tools for assessment. Two thirds of the studies addressing patients’ or clinicians’ research questions were not limited to particular conditions but were applicable more widely across health care such as nursing care or health services generally. The 27 formal studies of patient involvement revealed a literature that has grown in the last decade. Although only nine studies engaged patients and clinicians in identifying research questions together, they show that methods have advanced over time, with all of them engaging participants directly and repeatedly in facilitated debate, and most employing formal decision-making procedures. Conclusions: A sizeable literature is available to inform priorities for research and the methods for setting research agendas with patients and clinicians. This literature has yet to be appraised for the legitimacy and fairness of the participation methods or the quality of any evaluations. Nevertheless, the references are potentially useful to systematic reviewers and have been made publicly available alongside DUETS, the Database of Uncertainties of the Effects of Treatment, at www.library.nhs.uk/duets/.