Background: Congenital hypothyroidism is one of the commonest treatable endocrine diseases and can affect he growth and mental development of neonates. The neonatal screening program for congenital hypothyroidism has become a routine procedure in all developed countries and considered a monitoring tool for the early detection and therapy of hypothyroidism. In this study we investigated the prevalence and associated factors of congenital hypothyroidism in Duhok governorate of Kurdistan Region (Iraq).Methods: A cross-sectional study was conducted during the period from July 2014 to February2015. Capillary blood samples were obtained from 3000 newborn babies by heel prick and tested initially for the thyroid stimulating hormone (TSH) followed by assessing free thyroxine in those with TSH level >10 µIU/ml. Demographic and clinical data such as residency, ethnicity, mother age, newborn age, sex, maturity, birth weight, presence of congenital anomalies as well as related marriage and thyroid diseases of the mother were collected. Results: The number of neonates having TSH level >10µIU/ml was 88 resulting in a recall rate of 2.9%. Of the88 recalled neonates, 4 were diagnosed with congenital hypothyroidism (4.5%; 1 in 750 live births) and 7 with subclinical hypothyroidism (7.9%, 1 in 428 live births). There was significant association between the occurrence of congenital hypothyroidism and prematurity (p=0.04), congenital anomalies (p=0.03) and thyroid disease of the mother (p=0.03).Conclusions: The study sample showed a high prevalence of congenital hypothyroidism among neonates of Duhok governorate. Appropriate neonatal screening program and monitoring are essential to reduce the irreversible health consequences of this disorder.