Here we describe the process by which research questions were developed for reducing health risks for people with learning disabilities. A participatory approach was used to give service users and carers a clear voice in "deciding" questions, thereby setting the research agenda. Audio-taped interviews and focus groups were used. Forty people (20 service users, 10 carers, 10 care-workers) were recruited and gave consent for interview. Interviews incorporated scenarios and these were used to describe two different types of health risks (i) those relating to lifestyle, and (ii) those associated with unrecognized illness. Participants were invited to specify a research question for each scenario. A total of 78 questions were identified, and from these, six key themes emerged. The themes were validated using three separate focus groups (service users, carers, care-workers). From this process six final questions encompassing participants' key research concerns were produced. Questions were resubmitted to participants for prioritizing, using a postal voting system (75% response rate). The research clearly demonstrates that people with learning disabilities and carers can identify and prioritize research questions they consider significant for improving health.