Background: We systematically reviewed existing national child health research priorities in Sub-Saharan Africa, and the processes used to determine them. Methods: Collaborators from a purposive sample of 20 WHO-AFRO Region countries, assisted by key informants from a range of governmental, non-governmental, research and funding organisations and universities, identified and located potentially eligible prioritisation documents. Included documents were those published between 1990 and 2002 from national or nationally accredited institutions describing national health research priorities for child health, alone or as part of a broader report in which children were a clearly identifiable group. Laboratory, clinical, public health and policy research were included. Two reviewers independently assessed eligibility for inclusion and extracted data. Results: Eight of 33 potentially eligible reports were included. Five reports focused on limited areas of child health. The remaining three included child-specific categories in reports of general research priorities, with two such child-specific categories limited to reproductive health. In a secondary analysis of Essential National Health Research reports that included children, though not necessarily as an identifiable group, the reporting of priorities varied markedly in format and numbers of priorities listed, despite a standard recommended approach. Comparison and synthesis of reported priorities was not possible. Conclusions: Few systematically developed national research priorities for child health exist in sub-Saharan Africa. Children's interests may be distorted in prioritisation processes that combine all age groups. Future development of priorities requires a common reporting framework and specific consideration of childhood priorities.