To estimate the prevalence of CHD in Ecuador using the data available on national prevalence discharges—a population-based retrospective cohort study. Ecuador, conducted from 2000 to 2017. It reports 34,904 cases in 18 years, with a mean of 1939 cases discharged by year. It analyzed the ICD-10 codes Q20 to Q28. The five most common findings by a group and the order were cardiac septa Q21, defects of great arteries Q25, other congenital defects Q24, defects of cardiac chambers Q20, and circulatory system defects Q28. Defects of cardiac septa reported 9620 cases, followed by defects of the great arteries with 8585 cases. By specific pathology were patent ductus arteriosus with 6002, the discordance of atrioventricular connection 3227 cases, ventricular septum defect with 2831 cases, atrial septum defect with 2790 cases, arteriovenous malformation of cerebral vessels with 2419, and Fallot tetralogy with 2259 cases. The prevalence rate of CHD in Ecuador is 70.63/10,000 live births. It reports 34,904 cases in 18 years, with a mean of 1939 cases discharged by year. By specific pathology, the most common diagnostic was patent ductus arteriosus with 6002 cases. The most common CHD by the group was CHD of cardiac septa with 9620 cases, followed by CHD of the great arteries with 8585 cases. The year that reported more cases were 2013 with a mean prevalence rate of 97.5/10,000 live newborns, followed by the year 2015, with 94.5/10,000 live newborns.