The purpose of this study was to measure Greek hospital performance using different input-output combinations, and to identify the factors that influence their efficiency thus providing policy makers with valuable input for the decision-making process. Using a unique dataset, we estimated the productive efficiency of each hospital through a bootstrapped data envelopment analysis (DEA) approach. In a second stage, we explored, using a bootstrapped truncated regression, the impact of environmental factors on hospitals' technical and scale efficiency. Our results reveal that over 80% of the examined hospitals appear to have a technical efficiency lower than 0.8, while the majority appear to be scale efficient. Moreover, efficiency performance differed with inclusion of medical examinations as an additional variable. On the other hand, bed occupancy ratio appeared to affect both technical and scale efficiency in a rather interesting way, while the adoption of advanced medical equipment and the type of hospital improves scale and technical efficiency, correspondingly. The findings of this study on Greek hospitals' performance are not encouraging. Furthermore, our results raise questions regarding the number of hospitals that should operate, and which type of hospital is more efficient. Finally, the results indicate the role of medical equipment in performance, confirming its misallocation in healthcare expenditure.