Background: Congenital heart diseases are the most common congenital malformation with an incidence of approximately 8 per thousand live births. Congenital heart disease account for 6 to 10% of all infant deaths. Approximately 25% of children with congenital heart disease have critical congenital heart disease. Pulse oximetry in newborn screening can detect mild hypoxemia that may not be recognized by clinical examination. Thus pulse oximetry can help to identify babies that may be affected with critical congenital heart disease before they leave the newborn nursery. The objective of the present study were to determine the role of pulse oximetry as a screening tool for detection of congenital heart disease in newborns on the first day of life. Methods: This prospective study was conducted in the postnatal ward of department of Gynecology and obstetrics in SMGS Hospital Jammu over a period of one year from November 2016 to October 2017. In this study pulse oximetry and clinical examination were used as screening and echocardiography as a diagnostic/confirmatory tool for detection of congenital heart disease. Neonates were first subjected to clinical examination followed by pulse oximetry. Neonates having either or both of these screening methods positive were subjected to echocardiography. A total of 3213 newborns were screened. Results: Neonates with clinical examination suggestive of congenital heart disease (but normal pulse oximetry screening) were 16. On echocardiography, 7 were found to be normal and remaining 9 had CHD. Neonates with pulse oximetry screening suggestive of congenital examination (but normal clinical findings) were 9 and on echocardiography, among these 9 subjects, 7 had CHD and 2 had persistent pulmonary artery hypertension. 7 cases were both screening tests positive and all of these were detected with congenital heart disease on echocardiography. Thus total congenital clinical examination cases detected in our study were 23. The sensitivity, specificity, PPV and NPV of pulse oximetry was 60.87%, 77.78%, 87.50% and 43.75% respectively. The sensitivity, specificity, PPV and NPV of clinical examination was 69.57%.22.22%, 69.57% and 22.22% respectively. Conclusion: Pulse oximetry is an effective, non invasive and feasible screening tool for detection of congenital heart disease. Combining pulse oximetry screening and clinical examination can enhance clinician ability to detect life threatening CHD in a timely manner and this screening method should become a part of discharge policy of every newborn.