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Background: Considering the high prevalence of congenital hypothyroidism (CH) in Isfahan and its different etiologies comparing with other countries, the high rate of parental consanguinity and the role of DUOX2 gene in transient CH and permanent CH due to dyshormonogenesis, the aim of this research was to investigate the mutations of DUOX2 gene in patients with transient or permanent CH due to dyshormonogenesis. Methods: In this descriptive prospective study, patients diagnosed with transient CH and permanent CH due to dyshormonogenesis during CH screening program, were selected. Venous blood sample was obtained to determine the 3 mutations Q36H, R376W, D506N of DUOX2 gene using PCR method by specific primers and complementary methods such as Restriction fragment length polymorphism (RFLP) and Single-strand conformation polymorphism (SSCP). Finding: In this study 25 and 33 CH patients with transient CH and permanent CH due to dyshormonogenesis were studied respectively. 30 children studied as control group. We did not find any mutation of the mentioned three mutations of DUOX2 gene.   Conclusion: Considering the findings of current study, it seems that further studies with other methods and also with considering other gene mutations such as pendrin, NIS and thyroglobulin is needed for more accurate conclusion.