Screening critical congenital heart disease in neonates with 24-48 h of age could be made by oxygen saturation determination. Perfusion index may be used as an adjunct to pulse oximetry screening to detect non-cyanotic critical congenital heart disease cases such as a left heart outflow obstruction. We evaluate the results of combined screening for oxygen saturation and peripheral perfusion index at high altitudes. The study included 501 neonates older than gestational week 35. The mean oxygen saturation was lower than at sea level, and the screening test was positive in a total of 21 (4.2%) babies. Critical congenital heart diseases were not detected in any patient. A total of 10 (2%) babies were detected with PDA, nine (1.8%) of whom recorded a positive screening test. The prevalence of PDA was significantly higher in the positive screening test group when compared with those who underwent echocardiography due to clinical findings.