Screening for critical congenital heart disease is a clinical method used for their early detection using pulse oximetry technology. This, followed by a diagnostic confirmatory protocol, allows timely therapeutic interventions that improve the newborn's outcome. According to Mexican birth statistics, approximately 18,000-21,000 neonates are born with a form of congenital heart disease each year, of which 25% are estimated to be critical congenital heart disease. We report two cases with an early critical congenital heart disease detection and intervention through an innovative critical congenital heart disease screening program implemented in two Mexican hospitals. They integrated a new automated pulse oximetry data analysis method and a comprehensive follow-up system (Cárdi-k®). Both cases were confirmed by echocardiogram, which served for an intervention in the first week of life, and the patients were discharged in good clinical condition. In addition, to the routine physical assessments, the critical congenital heart disease screening program (which includes echocardiogram for presumptive positive cases) should be implemented in a timely manner.