The objective of this study was to evaluate combined pulse oximetry and clinical examination as a screening method for congenital heart disease (CHD) in asymptomatic newborns. Asymptomatic newborns were screened for CHD using pulse oximetry and clinical examination before their discharge from the nursery. Oxygen saturation ≥94% was considered normal. Echocardiography was done for newborns with abnormal readings and for those with significant murmurs. Data concerning undetected cases were collected from the pediatric referral hospital. A total of 5211 cases were screened. Echocardiographic evaluations were done based on low pulse oximetry in five cases and on murmur detection in ten others. The sensitivity of the combined method of screening was 77%, whereas it was 31% for oximetry alone and 46% for clinical examination alone. Specificity was ∼100% for all methods. The positive predictive value of the combined tool was 66.7%. We conclude that combining pulse oximetry and clinical examination can enhance the clinician’s ability to detect life-threatening CHD in a timely manner. This screening method should become a part of the discharge plan for every newborn.