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Background and purpose: Thalassemia is a preventable genetic disorder that is a major health problem. It is now two decades since implementation of the national program for preventing β-thalassemia major in Iran. This study was conducted to compare the costs and results of this program from 2010 to 2014 in Mazandaran University of Medical Sciences. Materials and methods: Economic evaluation was done in this descriptive analytic study. We extracted the data from surveillance reports of health deputy and costs of laboratory services from the private and public sectors and Legal Medicine Organization tariffs. Other cost items were determined using published reports and articles, and interviewing the administrators and researchers. All costs were calculated in Excel 2007 based on the economic value of 2014. Results: The total direct costs of medical services, direct non-medical and non-medical direct costs of implementation of national program for preventing β-thalassemia major in one year were over 18,418,872,744 Rials. The average cost of prevention of a β-thalassemia major birth case was estimated to be be 341,090,236 Rials. The cost ratio of prevention to treatment was 1:12. Five-year implementation of the national program prevented 270 babies born with thalassemia. The success rate of this program was 95% in Mazandaran. Conclusion: Cost benefit analysis showed that the national program for preventing β-thalassemia major was efficient and economically valuable in Mazandaran province.