Background: The spectrum of cardiac diseases in children is distinct from that in adults, and changes with advances in medical care and socioeconomic conditions. Such data are important for the allocation of medical resources, but are unclear. Based on a longitudinal pediatric cardiac screening program, we sought to delineate the spectrum and the trends. Methods: From 2002 to 2018, citywide screening programs of cardiac diseases for children were performed in Taipei, Taiwan. Participants, mainly students entering the first grade of elementary school, were evaluated using questionnaires, simplified 4-lead electrocardiography (EKG), phonocardiography, and physical examinations. Those suspected of having abnormal cardiac lesions received detailed evaluations by pediatric cardiologists for a final diagnosis. Results: The median prevalence of cardiac lesions in the children was 19.60/1000 (range from 14.9 to 24.65/1000), including congenital heart disease (32.02%), EKG abnormalities (33.34%), mitral valve prolapse (15.17%), Kawasaki disease (6.89%), rheumatic heart disease (0.17%) and others (12.41%). A significant time trend was only observed in a trend of decline in rheumatic heart disease. The median prevalence rates of congenital heart disease, Kawasaki disease, rheumatic heart disease, mitral valve prolapse, and EKG abnormalities were 6.20, 1.37, 0, 3.12, and 6.46 per 1000 children, respectively. Conclusions: This study, based on a citywide cardiac screening program, indicates that the spectrum of cardiac diseases in children has not changed in recent decades, except for a decline or disappearance of rheumatic heart disease in the Taipei metropolitan area. While congenital heart disease and EKG abnormalities were the most common, Kawasaki disease was the most commonly acquired heart disease in children.