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Background: Considering the role of maternal thyroid stimulating hormone (TSH) receptor blocking antibody (TRAb) in the etiology of congenital hypothyroidism (CH), this study aimed to determine TRAb among patients with CH in Isfahan, Iran., Methods: In this case-control study, patients with CH and their mothers were compared with a group of healthy neonates and their mothers. Venous blood samples were obtained for measurement of TRAb using enzyme-linked immunosorbent assay (ELISA) method among mothers and their neonates. TSH of mothers was also determined., Results: The case group consisted of 65 patients with CH and their mothers; controls were 148 healthy neonates and their mothers. The prevalence of positive TRAb in patients with CH and their mothers was higher than in the control group (81.5% vs. 1.3% in mothers and 80% vs. 0% in neonates, respectively, P<0.05). The relationship between the TRAb and occurrence of CH was significant (P<0.05), whereas the corresponding figure was not significant for TRAb and the level of maternal and neonatal TSH in case and control groups (P>0.05)., Conclusion: It seems that autoimmunity has an important role in the etiology of CH. Further studies are necessary to determine other autoantibodies in CH patients.