Introduction: Newborn sudden infant death syndrome (SIDS) has failed to decrease in the last decades, and a third of the neonatal cases occurred within the first 6 days of life. The long QT syndrome (LQTS) is a genetic disease with a prevalence of 1 in 2,000 live births and contributes to almost 10% of SIDS cases. Early identification of LQTS through electrocardiogram (ECG) screening is likely to reduce mortality. Methods and Results: In this ongoing prospective study we evaluated 2,251 ECGs from newborns participating in the KUNO Kids birth cohort study between July 2015 and July 2018. ECGs were recorded at a mean age of 2.0 days (IQR 0 days). The QT interval was corrected for heart rate using Bazett’s formula (QTc). A QTc between 451 and 460, 461–470, and >470 ms was measured in 23 (1.0), 14 (0.6), and 62 (2.8%) participants, respectively. Fourteen neonates (0.62%) were admitted and monitored because their initial QTc was ≥500 ms. In 2 genetically analyzed participants, a mutation was found. One disease-causing for LQTS type 1 and the other of unclear significance. Cascade screening revealed affected members in both families. Conclusion: A standardized neonatal ECG screening in the first days of life is able to identify neonates with a relevant transient form of prolonged QT intervals and to aid diagnosing congenital LQTS.