Introduction: In this era, the grate evolutions in management science, has made the existence of an evaluation system unavoidable, the lack of an evaluation system in organization considered as one of the organizational disease signs. This research aimed to study the evaluation system of Iran University Medical Sciences (IUMS) with Balance Score Cards. 

Methods: In this descriptive research we included all 50 managers, and heads of hospitals in IUMS in census sampling. SPSS software was used for data analyzing, and we used descriptive statistics for presenting findings.

Results: The general aspect with 66.67% and financial aspects with 33.83% had the most and the least scores. This shows that the current system has essantial weakness in all of evaluation aspects.

Conclusion: The present system had the major weakness points in all of aspects, and the most major weakness was at the financial one.