Research Support, Non-U.S. Gov't ; Journal Article ; BACKGROUND: The monitoring and evaluation of health research capacity strengthening (health RCS) commonly involves documenting activities and outputs using indicators or metrics. We sought to catalogue the types of indicators being used to evaluate health RCS and to assess potential gaps in quality and coverage. METHODS: We purposively selected twelve evaluations to maximize diversity in health RCS, funders, countries, and approaches to evaluation. We explored the quality of the indicators and extracted them into a matrix across individual, institutional, and national/regional/network levels, based on a matrix in the ESSENCE Planning, Monitoring and Evaluation framework. We synthesized across potential impact pathways (activities to outputs to outcomes) and iteratively checked our findings with key health RCS evaluation stakeholders. RESULTS: Evaluations varied remarkably in the strengths of their evaluation designs. The validity of indicators and potential biases were documented in a minority of reports. Indicators were primarily of activities, outputs, or outcomes, with little on their inter-relationships. Individual level indicators tended to be more quantitative, comparable, and attentive to equity considerations. Institutional and national-international level indicators were extremely diverse. Although linkage of activities through outputs to outcomes within evaluations was limited, across the evaluations we were able to construct potential pathways of change and assemble corresponding indicators. CONCLUSIONS: Opportunities for improving health RCS evaluations include work on indicator measurement properties and development of indicators which better encompass relationships with knowledge users. Greater attention to evaluation design, prospective indicator measurement, and systematic linkage of indicators in keeping with theories of change could provide more robust evidence on outcomes of health RCS.