Background: Deprivation indices are useful measures to analyze health inequalities. There are several methods to construct these indices, however, few studies have used Geographic Information Systems (GIS) and Multi-Criteria methods to construct a deprivation index. Therefore, this study applies Multi-Criteria Evaluation to calculate weights for the indicators that make up the deprivation index and a GIS-based fuzzy approach to create different scenarios of this index is also implemented. Methods: The Analytical Hierarchy Process (AHP) is used to obtain the weights for the indicators of the index. The Ordered Weighted Averaging (OWA) method using linguistic quantifiers is applied in order to create different deprivation scenarios. Geographically Weighted Regression (GWR) and a Morans I analysis are employed to explore spatial relationships between the different deprivation measures and two health factors: the distance to health services and the percentage of people that have never had a live birth. This last indicator was considered as the dependent variable in the GWR. The case study is Quito City, in Ecuador. Results: The AHP-based deprivation index show medium and high levels of deprivation (0,511 to 1,000) in specific zones of the study area, even though most of the study area has low values of deprivation. OWA results show deprivation scenarios that can be evaluated considering the different attitudes of decision makers. GWR results indicate that the deprivation index and its OWA scenarios can be considered as local estimators for health related phenomena. Morans I calculations demonstrate that several deprivation scenarios, in combination with the ‘distance to health services factor, could be explanatory variables to predict the percentage of people that have never had a live birth. Conclusions: The AHP-based deprivation index and the OWA deprivation scenarios developed in this study are Multi-Criteria instruments that can support the identification of highly deprived zones and can support health inequalities analysis in combination with different health factors. The methodology described in this study can be applied in other regions of the world to develop spatial deprivation indices based on Multi-Criteria analysis.