Background: A large number of newborns are affected by congenital heart diseases, which accounts for a high proportion of infant mortality worldwide. But there are regional variations in the prevalence and distribution pattern of congenital heart diseases. We evaluated the incidence, risk factors and diagnostic clues for congenital heart disease in newborns in our neonatal intensive care unit. Methods: A prospective observational study was conducted in the neonatal intensive care unit of Vydehi institute of medical sciences between January 2013 to December 2016. Congenital heart disease was suspected if clinical and confirmed by 2D echocardiography and doppler and colour flow imaging. Data was collected on a predesigned proforma containing information regarding gender, gestational age and weight at birth, family history, and associated malformations. Results: Out of 1974 babies screened for CHDs, 126 babies had CHDs (4.6%) of which 71(56%) were males. Most of neonates presented with Respiratory distress (52.3%), murmurs (49.5%), abnormal chest X ray (27.7%), followed by cyanosis (18.2%) in Cyanotic CHDs(100% of the cases). Conclusion: The incidence of CHD in newborns at the neonatal intensive care unit was higher than that in all live births.VSD was the most common congenital heart defect detected while Tetralogy of Fallot was commonest among the cyanotic heart defects.