Introduction:Efficiency is one of the most important indicators of hospital performance evaluation.Aim:The study was conducted to measure the efficiency of public hospitals.Material and methods:This was a cross-sectional and panel data study. Data were retrospectively collected using hospital records and hospital information system. In this study, panel data of 17 public hospitals affiliated with Ahvaz University of Medical Sciences, in southwest of Iran were studied during 2012-2016. The output-based data envelopment analysis technique and variable return to scale assumption (VRS) were used. Regression model was used to assess factors affecting hospital efficiency. Data were analyzed using Deap2.1 and R software.Results:The mean of technical efficiency, managerial efficiency, and scale efficiency of the hospitals during 2012-2016 were 0.230, 0.272 and 0.732, respectively. Assessment of return to scale results over 5 years showed that 65% (11 cases) of hospitals had a decreasing return to scale, 24% (4 cases) had a constant return to scale, and 12% (2 cases) had an increasing return to scale. Also, mean of technical managerial, and scale efficiency in specialized hospitals were higher than other hospitals (0.331, 0.353, and 0.873). Beta regression analysis showed the effect of both variable length of stay and number of beds on hospital efficiency was significant (p-value <0.05)..Conclusions:The results showed that efficiency of selected public hospitals was the poor. Technical efficiency and managerial efficiency were lower than scale efficiency rate. Also, Multi- specialized hospitals were in critical status considering resource management and economies of scale.