Background: Critical congenital heart disease (CCHD) constitutes a spectrum of different heart anomalies needing intervention early in life for survival. Pulse oximetry screening (POS) claims to have a sensitivity of 60%, specificity of 99.95%, positive predictive value (PPV) of 75% and a negative predictive value (NPV) of 99.98% in detecting CCHD.Objectives: To assess the effectiveness of POS in identifying CCHD in a tertiary care neonatal unit in Sri Lanka.Method: A prospective descriptive study was carried out at Sri Jayewardenepura General Hospital (SJGH) from October 2017 to March 2020 including all healthy newborns delivered at SJGH. Babies with a prenatal diagnosis of CHD and those who needed admission to neonatal unit before POS was performed were excluded. Recruited babies underwent POS after 24 hours, but before 48 hours of life, in addition to routine newborn examination.Results: There were 8964 live births during the study period. POS was carried out in 8718 babies and was positive in 19 babies; 18 babies had CHD confirmed by echocardiogram, out of which 14 had CCHD. Hence, the incidence of CCHD, identified by POS was 1.56 per 1000 live births. Furthermore, POS demonstrated a PPV of 73.7%, and a false positive rate of 0.06%.