Abstract Background Reducing health inequalities involves the identification and characterization of social and exposure factors and the way they accumulate in a given area. The areas of accumulation then allow for prioritization of interventions. The present study aims to build spatial composite indicators based on the aggregation of environmental, social and health indicators and their inter-relationships. Method Preliminary work was carried out firstly to homogenize spatial coverage, and secondly to study spatial variation of environmental (EI), socioeconomic (SI) and health (HI) indicators. The aggregation of the different indicators was performed using several methodologies for which results and decision-makers’ usability were compared. Results Four methodologies were tested: 1) A simple summation of normalized HI, EI and SI indicators (IC), 2) the sum of the normalized HI, EI and SI indicators weighted by the first principal component of a Principal Component Analysis (IC PCA), 3) the sum of normalized and weighted indicators of the first principal component of Local Principal Component Analysis (IC LPCA), and 4) the sum of normalized and weighted indicators of the first principal component of a Geographically Weighted Principal Component Analysis (IC GWPCA). Conclusion The GWPCA is particularly adapted to taking into account the spatial heterogeneity and the spatial autocorrelation between SI, EI and HI. This approach invalidates the basic assumptions of many standard statistical analyses. Where socioeconomic indicators present high deprivation and where they are associated with potential modifiable health determinants, decision-makers can prioritize these areas for reducing inequalities by controlling the socioeconomic and health determinants.