The fact that health care expenditures represent a substantial proportion of total public expenditure places an enormous pressure to cut costs. Towards this objective in the last five years, the Ministry of Health has an ongoing program of reforms in the public hospital sector. On the other hand, cost containment in the health care sector should be carried out without compromising the quantity and quality of services produced. This is even more pertinent in Greece, given the current economic crisis. One way to compensate for reduced budgets in order to maintain or even improve the level of health care services offered is through identification and elimination of possible sources of inefficiency. It is evident, for instance, that once inefficiency has been eliminated, the saved resources could be devoted to cover other areas of the health care system (improved quality care to patients, innovative technology, staff training). Hence, the establishment of specific and thoroughly researched criteria for measuring efficiency is extremely important. In this context, the present study constitutes an inter-temporal efficiency map for the technical performance of hospital activity in the context of the Greek NHS throughout the five-year period 2009–2013. The empirical findings can be used as a useful guide for both hospital managers and policy makers in their process to improve the health care system, in favor of the true beneficiaries, which are the patients and society in general.