Introduction: Hospital as one of the most important providing organization of health sector uses a high proportion of health sources, needs to measure its efficiency a must. This this study was aimed to estimate the efficiency of hospitals.

Methods: This descriptive study has done in 2008.The study population are all health centers and general hospitals affiliated Isfahan University of Medical Science in 2005-2006.Data are accumulated by the forms that the researches have been drawn according to their purposes. Input variables were the numbers of specialist doctors, physician, nurses and other personals and the numbers of beds the output variables were the average of patient residing, the bed turnover interval, the coefficient of bed occupy, the numbers of outpatient reception and the hospitals income. Data are analyzed by the software of DEAP 2.

Results: The average of total technical efficiency, managerial efficiency and scale efficiency of the hospitals with the method of placed minimizing were 0.938, 0.957 and 0.98 respectively for 2005 and 0.946, 0.964 and 0.981 respectively for 006. These figures with the method of fixed maximization were 0.931, 0.974 and 0.956 for 2005 and 0.868, 0.902 and 0.962 for 2006. 

Conclusion: Inefficient hospitals should prevent from resources wastes in optimal level with decreas- ing the excessive laid and increasing the fixed levels they can acquire an optimal function by using this way.