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Background: Critical congenital heart diseases (CCHDs) are among the most common birth malformations. This study aimed to determine the cardiac and noncardiac diseases in the Iranian healthy newborns using pulse oximetry (POX) as a suggested screening method.Methods: In this cross-sectional study, healthy term and near term neonates who were born from October 2017 to March 2018 were evaluated. Preductal and postductal POX was performed in all asymptomatic healthy newborns after 24 hours of life or at any time before discharge from the nursery. Oxygen saturation (SPO2) was considered normal if SPO2 was  95%, and the difference between preductal O2 saturation and postductal POX was obtained at ≤ 3%. The POX was repeated after 2 hours for abnormal patients. In the case of the same results in both repeated measures, echocardiography, chest X-ray, sepsis screening, and blood glucose were conducted.Results: A total of 413 asymptomatic healthy term and near term neonates underwent the pulse oximetry screening (POX). The mean birth weight and gestational age of the neonates were 3256.31±509.62 gr and 38.2 weeks, respectively. The POX was performed averagely 19.5 hours after birth. Finally, a total of 10 cases were detected with abnormal POX. Among these 10 patients, three cases had cardiac diseases (i.e., transposition of the great arteries, ventricular septal defect/pulmonary atresia, and ventricular septal defect/pulmonary hypertension), three cases had noncardiac diseases (i.e., esophageal stenosis, hypoglycemia, and persistent pulmonary hypertension/sepsis), and four subjects were healthy.Conclusion: The obtained findings showed that routine pox, along with clinical examinations could be applied, especially in developing countries for the early detection of cardiac and noncardiac diseases in asymptomatic newborns.