Background Congenital heart diseases (CHD) cause declining of functional capacity, cyanosis, arrhythmia, stroke, and death in adulthood. The screening for congenital heart disease in children has not been established in Indonesia. This results in a relatively high prevalence of uncorrected CHD in adulthood, who mostly have developed pulmonary artery hypertension. The screening program by cardiac auscultation and electrocardiography (ECG) in schoolchildren has been proven to be feasible in developed countries, which may also be feasible in Indonesia.Aim This study was planned to test and assess CHD screening methods based on electrocardiography examination in school children.Methods We conducted a screening program in first grade elementary school children in the Province of Yogyakarta, Indonesia. The schools were determined by purposive sampling. Trained general practitioners in community health centers participated in the screening. The physical examinations were done, which focused on cardiac auscultation and ECG examination. Those who had abnormal findings underwent trans-thoracic echocardiography to confirm the CHD.Results We collaborated with local governments in recruiting the participating community health centers and elementary schools. A total of 130 elementary schools from 5 districts in Yogyakarta Province were recruited, all without prior information on students’ presentation of symptoms.Conclusions This study is the first screening program that focuses on heart diseases in elementary school students in Indonesia. The success and feasibility of this program will give a valuable impact on preventing CHD complications during adulthood.