BACKGROUND: Policies to improve health status, tackle disease and ensure equitable access to healthcare should be informed by evidence derived from high-quality research. However, health research capacity is unevenly distributed across countries, as revealed by mapping exercises that have been undertaken to provide a basis for concerted action to strengthen capacity. This study systematically describes capacity to undertake health research in the countries of the former Soviet Union and south-eastern Europe and identifies the elements required to create a national health research system. METHODS: The mapping exercise comprised two elements: a survey of key informants in the respective countries and a bibliometric analysis of scientific publications in the field of public health. RESULTS: Our results confirm that health research remains a low priority in some countries of the WHO European Region. In these countries, most of the literature was produced by researchers outside the country, often to inform international donors. CONCLUSIONS: This study provides important information for countries seeking to initiate action to strengthen their research capacity. There is a need for a comprehensive strategy with sustained investment in training and career development of researchers. There is also a need to create new funding systems to provide financial support to those undertaking policy-relevant research. International collaboration and investment in mechanisms to bridge the gap between research and policy are urgently required.