We determined the prevalence of congenital hypothyroidism and the rate of consanguin-ity among parents of hypothyroid neonates among 93 381 neonates born in 17 hospitals in Isfahan from May 2002 to April 2005. Serum thyroxine (T4) and thyroid stimulating hormone (TSH) levels were measured on the 3rd-7th day of birth and neonates with abnormal levels were recalled and the levels reassessed. Those with TSH > or = 10 mlU/L and T4 < 6.5 microg/dL on the second assay were considered hypothyroid. In all, 1038 neonates were recalled and 274 were diagnosed as hypothyroid. There was a significant association between parental consanguinity and congenital hypothyroidism (P = 0.006); congenital hypothyroidism was commoner in neonates with 1st cousin parental consanguinity than 2nd cousin parental consanguinity (P = 0.008).