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Background  The ability to measure regional health inequalities across Europe and to build adequate population health indices depends significantly on the availability of reliable and comparable data at the regional level. Within the scope of the EU-funded project EURO-HEALTHY, a Population Health Index (PHI) was built. This model aggregates 39 indicators considered relevant by experts and stakeholders to evaluate and monitor population health on the regional level within the European Union (269 regions). The aim of this research was to assess the data availability for those indicators. As a subsequent aim, an adequate protocol to overcome issues arising from missing data will be presented, as well as key messages for both national and European statistical authorities meant to improve data collection on population health.    Methods  The methodology for the study includes three consecutive phases: (i) assessing the data availability for the respective indicators at the regional level for the last year available (ii) applying a protocol for missing data and completing the database and (iii) developing a scoring system ranging from 0 (no data available; worst) to 1 (all data available; best) to evaluate the availability of data by indicator and EU region.    Results  Although the missing data on the set of the PHI indicators was significant, the mean availability score for the EURO-HEALTHY PHI indicators is 0.8 and the regional availability score is 0.7, which reveal the strength of the indicators as well as the data completeness protocol for missing data.    Conclusions  This study provides a comprehensive data availability assessment for population health indicators from multiple areas of concern, at the EU regional level. The results highlight that the data completeness protocol and availability scores are suitable tools to apply on any indicator’s data source mapping. It also raises awareness to the urgent need for sub-national data in several domains and for closing the data gaps between and within countries. This will require policies clearly focused on improving equity between regions and a coordinated effort from the producers of data (the EU28 national statistics offices and EUROSTAT) and the stakeholders who design policies at EU, regional and local level.    Electronic supplementary material  The online version of this article (10.1186/s12963-019-0188-6) contains supplementary material, which is available to authorized users.

Evaluation of data availability on population health indicators at the regional level across the European Union