Between January 1981 and March 1994, neonatal screening for congenital hypothyroidism (CH) in Hokkaido prefecture, Japan, detected thirty-four cases of Down syndrome (DS) with thyroid dysfunction. Of these 34 infants, 14 were diagnosed as having CH and the rest had various degrees of transient thyroid dysfunction. The incidence of CH in DS is estimated to be 1 in 41, being about 100 times more frequent than in the general population. Nevertheless, the prevalence of thyroid dysfunction in infants with DS was lower than that previously described in older children with DS. Periodical examination of thyroid function in children with DS is therefore recommended.