Congenital Hypothyroidism (CH) is one of the most preventable causes of mental retardation and can be detected through neonatal screening; it is estimated 1200 CH patients are born in Iran, annually. The aim of this investigation was to provide a report on the outcome and estimate the cost benefit ratio of the screening Program implementation for CH in Iran based on the pilot study.Materials and Methods: The cost of the screening Program for CH for each newborn was based on data gathered from the pilot study of three provinces and the amount then multiplied by the number of births per year. The care cost of mentally retarded individuals is calculated based on the Welfare budget of caring for these people.Results: Total cost of implementation of the neonatal screening Program for CH during the first year is 16, 256, 400, 000 Rials ($ 2, 000, 000). The ratio of the cost of care for the children to the cost of implementation of the screening Program is about 1 to 16 and the ratio of the benefit (cost saving) to the implementation cost is 1 to 15.Conclusion: The neonatal screening Program for CH has a very high potential for implementation in the country. As a result, the implementation of the CH screening Program as the first screening of newborns provides a basis for better understanding and timely detection of CH and other metabolic diseases in Iran.