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Background: In recent years there have been calls to strengthen health sciences research capacity in African countries. This capacity can contribute to improvements in health, social welfare and poverty reduction through domestic application of research findings; it is increasingly seen as critical to pandemic preparedness and response. Developing research infrastructure and performance may reduce national economies' reliance on primary commodity and agricultural production, as countries strive to develop knowledge-based economies to help drive macroeconomic growth. Yet efforts to date to understand health sciences research capacity are limited to output metrics of journal citations and publications, failing to reflect the complexity of the health sciences research landscape in many settings.Methods: We map and assess current capacity for health sciences research across all 54 countries of Africa by collecting a range of available data. This included structural indicators (research institutions and research funding), process indicators (clinical trial infrastructures, intellectual property rights and regulatory capacities) and output indicators (publications and citations).Results: While there are some countries which perform well across the range of indicators used, for most countries the results are varied-suggesting high relative performance in some indicators, but lower in others. Missing data for key measures of capacity or performance is also a key concern. Taken as a whole, existing data suggest a nuanced view of the current health sciences research landscape on the African continent.Conclusion: Mapping existing data may enable governments and international organizations to identify where gaps in health sciences research capacity lie, particularly in comparison to other countries in the region. It also highlights gaps where more data are needed. These data can help to inform investment priorities and future system needs. [ABSTRACT FROM AUTHOR]