Pulse oximetry screening (POS) has been shown to be an effective, non-invasive investigation that can detect up to 50-70% of previously undiagnosed congenital heart defects (CHDs). The aims of this study were to assess the accuracy of POS in detection of CHDs and its impact on clinical practice. All eligible newborn infants born between 1 Jan 2015 and 31 Dec 2019 in a busy regional neonatal unit were included in this prospective observational study. A positive POS was classified as two separate measurements of oxygen saturation < 95%, or a difference of > 2% between pre- and post-ductal circulations. Overall, 23,614 infants had documented POS results. One hundred eighty nine (0.8%) infants had a true positive result: 6 had critical CHDs, 9 serious or significant CHDs, and a further 156/189 (83%) infants had significant non-cardiac conditions. Forty-three infants who had a normal POS were later diagnosed with the following categories of CHDs post-hospital discharge: 1 critical, 15 serious, 20 significant and 7 non-significant CHDs. POS sensitivity for detection of critical CHD was 85.7%, whereas sensitivity was only 33% for detection of major CHDs (critical and serious) needing surgery during infancy; specificity was 99.3%.Conclusion: Pulse oximetry screening showed moderate to high sensitivity in detection of undiagnosed critical CHDs; however, it failed to detect two-third of major CHDs. Our study further emphasises the significance of adopting routine POS to detect critical CHDs in the clinical practice. However, it also highlights the need to develop new, innovative methods, such as perfusion index, to detect other major CHDs missed by current screening tools. What is Known: • Pulse oximetry screening is cost effective, acceptable, easy to perform and has moderate sensitivity and high specificity in detection of critical congenital heart defects. • Pulse oximetry screening has been implemented many countries including USA for detection of critical congenital heart defects, but it is not currently recommended by the UK National Screening Committee. What is New: • To our knowledge, this is the first study describing postnatal detection and presentation of all the infants with congenital heart defects over a period of 5 years, including those not detected on the pulse oximetry screening, on the clinical practice. • It emphasises that further research required to detect critical congenital heart defects and other major CHDs which can be missed on the screening tools currently employed in clinical practice.