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While it is important to be able to evaluate and measure a country's performance in health research (HR), HR systems are complex and multifaceted in nature. As such, attempts at measurement can suffer several limitations which risk leading to inadequate indices or representations. In this study, we critically review common indicators of HR capacity and performance and explore their strengths and limitations. The paper is informed by review of data sources and documents, combined with interviews and peer-to-peer learning activities conducted with officials working in health and education ministries in a set of nine African countries. We find that many metrics that can assess HR performance have gaps in the conceptualisation or fail to address local contextual realities, which makes it a challenge to interpret them in relation to other theoretical constructs. Our study identified several concepts that are excluded from current definitions of indicators and systems of metrics for HR performance. These omissions may be particularly important for interpreting HR performance within the context and processes of HR in African countries, and thus challenging the relevance, utility, appropriateness and acceptability of universal measures of HR in the region. We discuss the challenges that scholars may find in conceptualising such a complex phenomenon-including the different and competing viewpoints of stakeholders, in setting objectives of HR measurement work, and in navigating the realities of empirical measurement where missing or partial data may necessitate that proxies or alternative indicators may be chosen. These findings are important to ensure that the global health community does not rely on over-simplistic evaluations of HR when analysing and planning for improvements in low-income and middle-income countries., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2021. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)