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© 2016 The Author(s). Background: Mental health disorders (MHDs) constitute a large and growing disease burden in Europe, although they typically receive less attention and research funding than other non-communicable diseases (NCDs). This study protocol describes a methodology for the mapping of MHD research in Europe as part of Mapping_NCD, a 2-year project funded by the European Commission which seeks to map European research funding and impact for five NCDs in order to identify potential gaps, overlaps, synergies and opportunities, and to develop evidence-based policies for future research. Methods: The project aims to develop a multi-focal view of the MHD research landscape across the 28 European Union Member States, plus Iceland, Norway and Switzerland, through a survey of European funding entities, analysis of research initiatives undertaken in the public, voluntary/not-for-profit and commercial sectors, and expert interviews to contextualize the gathered data. The impact of MHD research will be explored using bibliometric analyses of scientific publications, clinical guidelines and newspaper stories reporting on research initiatives. Finally, these research inputs and outputs will be considered in light of various metrics that have been proposed to inform priorities for the allocation of research funds, including burden of disease, treatment gaps and cost of illness. Discussion: Given the growing burden of MHDs, a clear and broad view of the current state of MHD research is needed to ensure that limited resources are directed to evidence-based priority areas. MHDs pose a particular challenge in mapping the research landscape due to their complex nature, high co-morbidity and varying diagnostic criteria. Undertaking such an effort across 31 countries is further challenged by differences in data collection, healthcare systems, reimbursement rates and clinical practices, as well as cultural and socioeconomic diversity. Using multiple methods to explore the spectrum of MHD research funding activity across Europe, this project aims to develop a broad, high-level perspective to inform priority setting for future research.