The main objective of this study was to apply DEA to measure the efficiency of the Greek NHS hospitals during the period 2009–2013. The hospitals were categorized and allocated into four separate groups with common characteristics in order to increase their homogeneity. The DEA-Windows method was chosen for the assessment of their efficiency since (a) it leads to increased discrimination on the results especially when applied on small samples and (b) provides a means for the year-to-year comparison of the results. At the same time, the number of DMUs is doubled since, in essence, every actual hospital participates twice in each window and therefore the discrimination of the method is improved.