Introduction Health facilities assessments are an essential instrument for health system strengthening in low- and middle-income countries. These assessments are used to conduct health facility censuses to assess the capacity of the health system to deliver health care and to identify gaps in the coverage of health services. Despite the valuable role of these assessments, there are currently no minimum standards or frameworks for these tools.Methods We used a structured keyword search of the MEDLINE, EMBASE and HealthStar databases and searched the websites of the World Health Organization, the World Bank and the International Health Facilities Assessment Network to locate all available health facilities assessment tools intended for use in low- and middle-income countries. We parsed the various assessment tools to identify similarities between them, which we catalogued into a framework comprising 41 assessment domains.Results We identified 10 health facility assessment tools meeting our inclusion criteria, all of which were included in our analysis. We found substantial variation in the comprehensiveness of the included tools, with the assessments containing indicators in 13 to 33 (median: 25.5) of the 41 assessment domains included in our framework. None of the tools collected data on all 41 of the assessment domains we identified.Conclusions Not only do a large number of health facility assessment tools exist, but the data they collect and methods they employ are very different. This certainly limits the comparability of the data between different countries’ health systems and probably creates blind spots that impede efforts to strengthen those systems. Agreement is needed on the essential elements of health facility assessments to guide the development of specific indicators and for refining existing instruments.