Congenital anomalies, also known as birth defects, are a significant public health concern worldwide. They contribute significantly to the global burden of disease, with congenital heart defects being the leading cause of mortality and morbidity among birth defects. Over the years, advancements in diagnosis and treatment have led to a decline in the disease burden associated with these anomalies. Belgium has seen limited national efforts to investigate the burden of disease, especially regarding congenital anomalies. While global estimates provide a general overview of the disease burden in Belgium, the extent to which these estimates are based on reliable, local data remains uncertain. This study aims to evaluate the quality of various national data sources that provide information on the occurrence of congenital anomalies. The most reliable data source is then used to determine prevalence figures, which serve as the basis for further calculations that will help understand the impact of these conditions more accurately. The study focuses specifically on congenital heart defects, which are the most common type of birth defects and significantly contribute to the overall burden of congenital anomalies. Disability-adjusted life years (DALYs) are used to assess the health impact of congenital heart defects, which can be defined as the number of healthy life years lost to disease, disability and death. In 2019, a prevalence of 79.33 cases per 10,000 births was reported for congenital heart defects in Belgium. During the same period, these defects resulted in a total of 2,579 DALYs. Among the different types of congenital heart defects, ventricular septal defects have been found to be more prevalent year after year and have emerged as the primary contributor to the overall health burden associated with congenital heart defects. The results of this study were lower than those based on other, broader sources of disease burden estimates. This study relied on the calculation methods outlined by Sciensano in the Belgian National Burden of Disease Study, which uses a more systematic approach that includes comparable estimates rooted in recent, local data. In contrast to the declining trend of disease burden over the years seen both globally and nationally, it was noted that the prevalence of congenital heart defects has increased by 49% since 2012. This underscored the need for more research into population-level factors that can be employed to improve the prevention of this disease. This study reviewed available epidemiological information, assessed data quality, and followed a systematic approach to estimate the burden of disease utilizing local, recent data to generate health estimates. The findings can guide the development of targeted public health interventions to prevent, detect, and manage congenital anomalies, ultimately reducing their occurrence and their physical and psychosocial impact on affected individuals, families, and society.