The aim of our study was to investigate the incidence of congenital defects in children born in Croatia during a period of 5 years, its association with extracardiac malformations, its treatment, and outcome. Medical information about the patients was obtained from 14 paediatric cardiology centres that cover the whole country. Diagnosis was made by clinical findings, electrocardiography, chest X-ray, echocardiography, catheterisation, or autopsy. Between October 1, 2002 and October 1, 2007, there were 205,051 live births in Croatia, 1,480 of which were patients diagnosed with congenital heart disease, accounting for 0.72% of the live-born children. The distribution was made up of 34.6% children with ventricular septal defect, 15.9% with atrial septal defect, 9.8% with patency of arterial duct, 4.9% with pulmonary valvar stenosis, 3.3% with tetralogy of Fallot, 3.3% with transposed great arteries, 3.3% with aortic stenosis, 3.2% with aortic coarctation, 4.3% with atrioventricular septal defect and common atrioventricular orifice, 2.3% with hypoplastic left heart syndrome, and 8.3% other with severe defects. The average age in the time of diagnoses is 70.41 days (SD, 188.13), with low average time of diagnoses of severe heart defects, 9.6 days (SD, 32.52). Among patients, 14.5% had chromosomal defects, syndromes, and/or other congenital major anomalies. During the study, 57 patients died because of cardiac anomalies or other related problems, 24 who died were operated. The rates of specific cardiac defects and association with extracardiac malformations are generally comparable with those reported in similar studies. In spite of all problems, mortality rate of 3.85% is low but could be improved.