BACKGROUND: Health policy and systems research and analysis (HPSR+A) has been noted as central to health systems strengthening, yet the capacity for HPSR+A is limited in low- and middle-income countries. Building the capacity of African institutions, rather than relying on training provided in northern countries, is a more sustainable way of building the field in the continent. Recognising that there is insufficient information on African capacity to produce and use HPSR+A to inform interventions in capacity development, the Consortium for Health Policy and Systems Analysis in Africa (2011-2015) conducted a study with the aim to assess the capacity needs of its African partner institutions, including Nigeria, for HPSR+A. This paper provides new knowledge on health policy and systems research assets and needs of different stakeholders, and their perspectives on HPSR+A in Nigeria. METHODS: This was a cross-sectional study conducted in the Enugu state, south-east Nigeria. It involved reviews and content analysis of relevant documents and interviews with organizations' academic staff, policymakers and HPSR+A practitioners. The College of Medicine, University of Nigeria, Enugu campus (COMUNEC), was used as the case study and the HPSR+A capacity needs were assessed at the individual, unit and organizational levels. The HPSR+A capacity needs of the policy and research networks were also assessed. RESULTS: For academicians, lack of awareness of the HPSR+A field and funding were identified as barriers to strengthening HPSR+A in Nigeria. Policymakers were not aware of the availability of research findings that could inform the policies they make nor where they could find them; they also appeared unwilling to go through the rigors of reading extensive research reports. CONCLUSION: There is a growing interest in HPSR+A as well as a demand for its teaching and, indeed, opportunities for building the field through research and teaching abound. However, there is a need to incorporate HPSR+A teaching and research at an early stage in student training. The need for capacity building for HPSR+A and teaching includes capacity building for human resources, provision and availability of academic materials and skills development on HPSR+A as well as for teaching. Suggested development concerns course accreditation, development of short courses, development and inclusion of HPSR+A teaching and research-specific training modules in school curricula for young researchers, training of young researchers and improving competence of existing researchers. Finally, we could leverage on existing administrative and financial governance mechanisms when establishing HPSR+A field building initiatives, including staff and organizational capacity developments and course development in HPSR+A.