Context:Congenital hypothyroidism (CH) is one of the most common preventable causes of mental retardation in children and it occurs in approximately 1:2,000-1:4,000 newborns.Aims and Objectives:The aim of this study is to determine the frequency of CH in neonates.Settings and Design:This cross-sectional study was conducted in neonatal units of the Department of Pediatrics Unit-I, King Edward Medical University/Mayo Hospital, Lahore and Lady Willington Hospital Lahore in 6 months (January-June 2011).Materials and Methods:Sample was collected by non-probability purposive sampling. After consent, 550 newborn were registered for the study. Demographic data and relevant history was recorded. After aseptic measures, 2-3 ml venous blood analyzed for thyroid-stimulating hormone (TSH) level by immunoradiometric assay. Treatment was started according to the individual merit as per protocol.Statistical Analysis Used:Data was analyzed by SPSS 17 and Chi-square test was applied to find out the association of CH with different variables.Results:The study population consisted of 550 newborns. Among 550 newborns, 4 (0.8%) newborns had elevated TSH level. CH had statistically significant association with mother's hypothyroidism (P value 0.000) and mother's drug intake during the pregnancy period (P value 0.013).Conclusion:CH is 0.8% in neonates. It has statistically significant association with mother's hypothyroidism and mother's drug intake during pregnancy.