PURPOSE: Congenital hypothyroidism (CH) is the most common neonatal endocrine disorder, however, its molecular etiology remains poorly understood. METHODS: We performed genetic analysis of 24 causative genes using next-generation sequencing in 167 CH cases (57 dyshormonogenesis (DH), 32 dysgenesis (TD) and 78 undiagnosed). The pathogenicity of variants was assessed by the American College of Medical Genetics guidelines, inheritance pattern and published evidence. Further, we compared the oligogenic groups and monogenic groups to examine the correlation between variant dosage and severity. RESULTS: We identified variants in 66.5% cases (111/167) and fifteen genes, DUOX2, TSHR, PAX8, TG, TPO, DUOXA2, JAG1, GLIS3, DUOX1, IYD, SLC26A4, SLC5A5, SECISBP2, DIO1, and DIO3. Biallelic variants were identified in 12.6% (21/167), oligogenic in 18.0% (30/167), and monogenic in 35.9% (60/167), however, 68.5% of variants were classified as variant of unknown significance (VUS). Further examinations showed that three out of 32 cases with TD (9.4%) had pathogenic variants (two of TSHR and one of TPO), eight out of 57 cases with DH (14.0%) (seven of DUOX2, one of TG) had pathogenic variants. In addition, TSH levels at the first visit were significantly higher in the oligogenic group than in the monogenic group. CONCLUSIONS: The detection rate of pathogenic variants in Japanese CH was similar to that previously reported. Moreover, oligogenic cases were likely to be more severe than monogenic cases, suggesting that CH may exhibit a gene dosage effect. Further analysis of VUS pathogenicity is required to clarify the molecular basis of CH.