Congenital hypothyroidism may cause irreversible intellectual disability or failure to thrive if left untreated. Because this disorder can be prevented by early identification and early treatment, newborn mass screening started in 1979 in Japan. A guideline for mass screening for this disease was prepared in 1998. Currently, approximately 100% of newborns undergo this mass screening. The screening results show significant improvement of the intellectual outcome of patients with this disease, with almost no patients having irreversible intellectual disturbance or failure to thrive. However, there are issues of a delayed increase in thyroid stimulating hormone, management of latent hypothyroidism, and detection of central hypothyroidism. In recent years, as studies on this disease have advanced at the molecular level, many causative genes have been reported, clarification of the etiology, pathology, and clinical features has progressed, and new findings have been obtained.