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Humanitarian crises are associated with an increase in mental disorders and psychological distress. Despite the emerging consensus on intervention strategies in humanitarian settings, the field of mental health and psychosocial support (MHPSS) in humanitarian settings lacks a consensus-based research agenda.From August 2009 to February 2010, we contacted policymakers, academic researchers, and humanitarian aid workers, and conducted nine semistructured focus group discussions with 114 participants in three locations (Peru, Uganda, and Nepal), in both the capitals and remote humanitarian settings. Local stakeholders representing a range of academic expertise (psychiatry, psychology, social work, child protection, and medical anthropology) and organizations (governments, universities, nongovernmental organizations, and UN agencies) were asked to identify priority questions for MHPSS research in humanitarian settings, and to discuss factors that hamper and facilitate research.Thematic analyses of transcripts show that participants broadly agreed on prioritized research themes in the following order: (1) the prevalence and burden of mental health and psychosocial difficulties in humanitarian settings, (2) how MHPSS implementation can be improved, (3) evaluation of specific MHPSS interventions, (4) the determinants of mental health and psychological distress, and (5) improved research methods and processes. Rather than differences in research themes across countries, what emerged was a disconnect between different groups of stakeholders regarding research processes: the perceived lack of translation of research findings into actual policy and programs; misunderstanding of research methods by aid workers; different appreciation of the time needed to conduct research; and disputed universality of research constructs.To advance a collaborative research agenda, actors in this field need to bridge the perceived disconnect between the goals of “relevance” and “excellence.” Research needs to be more sensitive to questions and concerns arising from humanitarian interventions, and practitioners need to take research findings into account in designing interventions.