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Background: There has been growing interest in the contribution of non-governmental organisations (NGOs) to international health research. One strength that NGOs may bring to research involves the potential value of service delivery experience for indicating relevant research questions, namely through their involvement in service delivery, NGO staff may be aware of frontline knowledge gaps, allowing these staff to identify questions that lead to research with immediate relevance. However, there is little empirical evidence on research agendas within NGOs to assess whether their service delivery experience does lead to relevant research or conditions that affect this. This article examines the identification and selection of research questions within NGOs to explore the role of their service delivery experience in generating relevant research agendas.Methods: The article reports comparative case study research on four NGOs in Malawi, including two international and two Malawian organisations. Each NGO conducts research and undertakes service delivery and advocacy. Data collection included interviews, focus groups, observation and document review. Analysis involved thematic coding and use of diagrams.Results: The case NGOs' experiences suggest that using service delivery to identify research questions does not always match NGOs' aims or capacities, and does not guarantee relevance. First, NGOs do not want to rely only on service delivery when developing research agendas; they consider other criteria and additional sources of ideas when selecting questions they see as relevant. Second, service delivery staff are not always well-placed to identify research topics; indeed, involvement in hectic, target-driven service delivery can hinder input to research agendas. Third, NGOs' ability to pursue questions inspired by service delivery depends on control over their research agendas; relationships with external actors and financial autonomy affect NGOs' capacity to undertake the research they see as relevant. Finally, the perceived relevance of research findings varies between audiences and depends on more than the research question.Conclusions: The findings suggest limits to the value and feasibility of a research agenda based on service delivery experience. Based on the analysis, the conclusion outlines strategies to support an effective role for NGOs' service delivery experience in development of research agendas. [ABSTRACT FROM AUTHOR]