In this paper we summarize the development of the official registration program of congenital anomalies in the Czech Republic from its beginnings in 1964 to present state. The historical review shows all running changes in the registration process that always reflected the actual knowledge in the epidemiology of congenital anomalies. The quantitative changes include mainly the change in the numbers of registered diagnoses. The qualitative changes include the increase of the age limit at diagnoses from original 7 days to current 15 years of age and the association of the prenatally diagnosed cases with the core database. During the 45 years of consecutive monitoring of the congenital anomalies in the Czech Republic we have determined the incidences of severe congenital anomalies in the population and we have analyzed the trends in these incidences (using both time and territory criteria). In the conclusion we discuss the role of the registration in the National health information system and the importance for the healthcare quality monitoring.