Background: The European Union health policy agenda stresses the importance of environmental and qualitative factors in structural hospital reforms. In response to the economic crisis, both cost containment and performance improvements of the Greek hospital sector, have become a pertinent issue for overall reforms.Objective: The study examines the efficiency of 112 Greek public hospitals, by applying bootstrapping techniques and investigating the effect of contextual factors on hospital efficiency. Furthermore, the effect of qualitative evidence, on hospital efficiency is explored by focusing on a subset of 28 large hospitals.Methods: The quality aspects of the Greek hospitals are investigated by applying two models of Data Envelopment Analysis (DEA), augmented by bootstrapping techniques, in order to assess the importance of quality dimensions on the efficiency of hospital scores. In addition, two Tobit regression models are estimated assessing the contribution of contextual factors, in the efficiency and bias-corrected efficiency scores.Results: Efficiency analysis indicated that only 23.2% of the hospitals are fully efficient (0.96-1.00), 37.5% are efficient (0.71-0.95) while 39.3% are inefficient (0.30-0.70). The Kolmogorov-Smirnov test, between the original and the bootstrap-corrected efficiency, indicates that their distributions are significantly different (p-value < .001). The environmental factors, influencing efficiency, are Occupancy Rate and the ratio between Outpatient Visits and Inpatient Days. Results indicate that the inclusion of Risk-Adjustment Mortality Rate significantly influences (p-value < .05) the efficiency of the hospitals.Conclusions: In the era of economic crisis, the inclusion of quality variables and the use of bootstrapping techniques provide a vital framework in assessing the efficiency of the hospital sector.