Background: Health research capacity strengthening (RCS) projects are often complex and hard to evaluate. In order to inform health RCS evaluation efforts, we aimed to describe and compare key characteristics of existing health RCS evaluation frameworks: their process of development, purpose, target users, structure, content and coverage of important evaluation issues. A secondary objective was to explore what use had been made of the ESSENCE framework, which attempts to address one such issue: harmonising the evaluation requirements of different funders. Methods: We identified and analysed health RCS evaluation frameworks published by seven funding agencies between 2004 and 2012, using a mixed methods approach involving structured qualitative analyses of documents, a stakeholder survey and consultations with key contacts in health RCS funding agencies. Results: The frameworks were intended for use predominantly by the organisations themselves, and most were oriented primarily towards funders' internal organisational performance requirements. The frameworks made limited reference to theories that specifically concern RCS. Generic devices, such as logical frameworks, were typically used to document activities, outputs and outcomes, but with little emphasis on exploring underlying assumptions or contextual constraints. Usage of the ESSENCE framework appeared limited. Conclusions: We believe that there is scope for improving frameworks through the incorporation of more accessible information about how to do evaluation in practice; greater involvement of stakeholders, following evaluation capacity building principles; greater emphasis on explaining underlying rationales of frameworks; and structuring frameworks so that they separate generic and project-specific aspects of health RCS evaluation. The third and fourth of these improvements might assist harmonisation. © 2013 Boyd et al.; licensee BioMed Central Ltd.