Monitoring the performance of hospitals is a crucial issue related both with the quality of healthcare services and with country’s economy. An easy and trustful way of evaluating health systems is through key performance indicators (KPIs). Such indicators are widely used for the identification of gaps in the quality or efficiency of the services provided. The main aim of this study is the analysis of the financial and operational indicators at hospitals in the 3rd and 5th Healthcare Regions of Greece. In addition, through cluster analysis and data visualization we attempt to uncover hidden patterns that may lie within our data. The results of the study support the need for re-evaluation of the assessment methodology of Greek hospitals to identify the weaknesses in the system, while evidently unsupervised learning exposes the potential of group-based decision making.