Congenital anomalies contribute to perinatal and infant mortality, often require medical care, and can affect the quality of life of affected children. This report presents indicators on congenital anomalies in France for the period 2019–2021, based on data analysis from five population-based registries (Antilles, Auvergne, Bretagne, La Réunion, Paris). These registries, which currently cover 16.4% of births in France, ensure continuous and comprehensive case recording according to the standardized criteria of the EUROCAT network. The main findings from this first combined analysis of data from multiple registries are: 1) In the areas covered by the 5 registries, 1 case per 28 total births (3.5%) was diagnosed with at least one major congenital anomaly. 2) The most frequent groups of congenital anomalies were cardiac anomalies, genetic (chromosomal and other) anomalies, and limb anomalies. 3) Nearly 60% of congenital anomalies were diagnosed prenatally, with a particularly high frequency for abdominal wall, renal, genetic, central nervous system, and complex cardiac anomalies, exceeding 75%. 4) Among cases diagnosed with at least one congenital anomaly, 74.4% were liveborn, 24.1% resulted in a termination of pregnancy for fetal anomaly (TOPFA), and 1.5% were stillborn. The groups of congenital anomalies most frequently leading to TOPFA were genetic anomalies, central nervous system anomalies, and cardiac anomalies. 5) Having a pregnancy affected by at least one genetic disorder was eight times higher in mothers aged 40 years and older compared to those 24 years and younger. This report provides an updated overview of key indicators on congenital anomalies to guide public health policies. In the short term, the epidemiological surveillance system will be strengthened by incorporating data from the Rhône-Alpes and Nouvelle-Aquitaine registries into the analyses. In the medium term, national coverage is envisioned, particularly through the development of detection algorithms within the National Health Data System (SNDS). This reinforcement is necessary in light of evolving risk factors, such as increasing maternal and paternal age, preconceptional obesity, or gestational diabetes, as well as environmental exposures, which may influence the frequency of certain anomalies.