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A regional disparity is becoming increasingly important growth constraint. Policy makers need quantitative knowledge to design effective and targeted policies. In this paper, the regional efficiency of healthcare facilities in Slovakia is measured (2008-2015) using data envelopment analysis (DEA). The DEA is the dominant approach to assessing the efficiency of the healthcare system but also other economic areas. In this study, the window approach is introduced as an extension to the basic DEA models to evaluate healthcare technical efficiency in individual regions and quantify the basic regional disparities and discrepancies. The window DEA method was chosen since it leads to increased discrimination on results especially when applied to small samples and it enables year-by-year comparisons of the results. Two stable inputs (number of beds, number of medical staff), three variable inputs (number of all medical equipment, number of magnetic resonance (MR) devices, number of computed tomography (CT) devices) and two stable outputs (use of beds, average nursing time) were chosen as production variable in an output-oriented 4-year window DEA model for the assessment of technical efficiency in 8 regions. The database was made available from the National Health Information Center and the Slovak Statistical Office, as well as from the online databases Slovstat and DataCube. The aim of the paper is to quantify the impact of the non-standard Data Envelopment Analysis (DEA) variables as the use of medical technologies (MR, CT) on the results of the assessment of the efficiency of the healthcare facilities and their adequacy in the evaluation of the monitored processes. The results of the analysis have shown that there is an indirect dependence between the values of the variables over time and the results of the estimated efficiency in all regions. The regions that had low values of the variables over time achieved a high degree of efficiency and vice versa. Interesting knowledge was that the gradual addition of variables number of MR, number of CT and number of medical devices together, to the input side did not have a significant impact on the overall estimated efficiency of healthcare facilities.