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Background: The aim of this study is to define the research capacity and training needs for professionals working on non-communicable diseases (NCDs) in the public health arena in Turkey. Methods: This study was part of a comparative cross-national research capacity-building project taking place across Turkey and the Mediterranean Middle East (RESCAP-Med, funded by the EU). Identification of research capacity and training needs took place in three stages. The first stage involved mapping health institutions engaged in NCD research, based on a comprehensive literature review. The second stage entailed in-depth interviews with key informants (KIs) with an overview of research capacity in public health and the training needs of their staff. The third stage required interviewing junior researchers, identified by KIs in stage two, to evaluate their perceptions of their own training needs. The approach we have taken was based upon a method devised by Hennessy&Hicks. In total, 55 junior researchers identified by 10 KIs were invited to participate, of whom 46 researchers agreed to take part (84%). The specific disciplines in public health identified in advance by RESCAP-MED for training were: advanced epidemiology, health economics, environmental health, medical sociology anthropology, and health policy. Results: The initial literature review showed considerable research on NCDs, but concentrated in a few areas of NCD research. The main problems listed by KIs were inadequate opportunities for specialization due to heavy teaching workloads, the lack of incentives to pursue research, a lack of financial resources even when interest existed, and insufficient institutional mechanisms for dialogue between policy makers and researchers over national research priorities. Among junior researchers, there was widespread competence in basic epidemiological skills, but an awareness of gaps in knowledge of more advanced epidemiological skills, and the opportunities to acquire these skills were lacking. Self-assessed competencies in each of the four other disciplines considered revealed greater training needs, especially regarding familiarity with the qualitative research skills for medical anthropology/sociology. Conclusions: In Turkey there are considerable strengths to build upon. But a combination of institutional disincentives for research, and the lack of opportunities for the rising generation of researchers to acquire advanced training skills. [ABSTRACT FROM AUTHOR]