Following elimination of iodine deficiency in Iran, the program of screening for congenital hypothyroidism (CH) was established in 1998. The descriptive findings of the study are reported here.From February 1998 to June 2001, cord blood spot samples from 8 hospitals and a rural birth center in Tehran and Damavand were collected and tested for TSH measurement using a two-site IRMA method. TSH values > or = 20 microU/mL were recalled. The diagnosis of CH was confirmed using age adjusted reference values for serum TSH and T4 levels.Of 20107 screened neonates, 256 had cord TSH values > or = 20 microU/mL (recall rate: 1.3%) and 22 showed hypothyroidism (1:914 live births). History of maternal ingestion of drugs and dietary goitrogens were negative and minimal, respectively. 15 out of 21 CH neonates had parental consanguinity. The odds ratio of CH occurrence in blood-related to non-related marriages was 6.9 (CI=1.82-25.87). Thyroid dysgenesis occurred in 10 neonates; 1:2011 births. Urinary iodine excretion was between 12-22 (n=3) and 40-42.5 (n=5) microg/dL in 10 eutopic neonates (2 not assessed).Parental consanguinity and iodine excess could be the causative factors for the high incidence of CH.