Congenital anomalies contribute to perinatal and infant mortality, frequently require medical care, and can impair the quality of life of the children affected. This report presents indicators on congenital anomalies in France for the period 2019–2021, based on an analysis of data from five population-based registries (the French West Indies, Auvergne, Brittany, Réunion, and Paris). These registries, which currently cover 16.4% of births in France, ensure continuous and comprehensive recording of cases according to the standardized criteria of the EUROCAT network. The main findings of this first combined analysis of data from multiple registries are: 1) In the areas covered by the five registries, 1 in every 28 total births (or 3.5%) was diagnosed with at least one major congenital anomaly. 2) The most common groups of congenital anomalies were heart defects, genetic anomalies (chromosomal and other), and limb anomalies. 3) Nearly 60% of congenital anomalies were diagnosed prenatally, with a particularly high rate—exceeding 75%—for abdominal wall, renal, genetic, central nervous system, and complex cardiac anomalies. 4) Among cases diagnosed with at least one congenital anomaly, 74.4% were born alive, 24.1% were subject to a medically indicated termination of pregnancy (MITP), and 1.5% were stillborn. The groups of congenital anomalies that most frequently led to a medical termination of pregnancy were genetic anomalies, central nervous system anomalies, and cardiac anomalies. 5) The prevalence of children with at least one genetic anomaly was 8 times higher when the mother was 40 years of age or older than when she was under 25 years of age. 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 including data from the Rhône-Alpes and Nouvelle-Aquitaine registries in the analyses. In the medium term, nationwide coverage is planned, notably through the development of detection algorithms within the National Health Data System (SNDS). This strengthening is necessary in light of changing risk factors, such as increasing maternal and paternal age, preconception obesity, or gestational diabetes, as well as environmental exposures, which could influence the incidence of certain anomalies.