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Introduction: Due to the development and the importance of universities of medical sciences in education system in Iran, this study was performed to rate universities of medical sciences in the field of education based on inputs and outputs. Methods: In This descriptive analytical study, educational efficiency of 41 universities of medical sciences was reviewed and analyzed using 4 inputs and 2 outputs in year 2008 through the method of Data Envelopment Analysis. Results: The results of types of efficiency measurement showed that 25 and 32 percent of universities of medical sciences had 100 percent technical and managerial efficiency, respectively. Seventy one percent of studied units did not act in optimal scale efficiency. The average technical efficiency of universities under investigation was 73 persent. Conclusion: Considering the capacity of 27 percent for increase of efficiency in the studied units, a proper planning using better efiiciency patterns and eficiency endorsement objectives could be applied for deficient universities.