OBJECTIVE: To describe the prevalence of congenital anomalies in children born in Amsterdam and to analyse potential differences between groups based on risk factors such as ethnicity and maternal age. DESIGN: Secondary analysis of a prospective cohort study. METHODS: Between 2003 and 2004, mothers filled in questionnaires on their newborn children on behalf of the Amsterdam-Born Children and their Development study (ABCD study). Data from 5,276 liveborn children in this cohort were used to calculate the prevalence rates of congenital anomalies in Amsterdam. These were compared with expected prevalence rates based on Eurocat data for the Northern region of the Netherlands during the years 2000-2005. Prevalence rates were compared between subgroups which had been divided according to risk factors: maternal ethnic origin, maternal age, parity, gender of child, inter-pregnancy interval, years of maternal education, smoking, alcohol use, and periconceptional folate use. RESULTS: The total prevalence of major congenital anomalies among liveborn children in the ABCD cohort was as expected based on the figures from the Eurocat registration. Digestive anomalies were reported significantly less frequently (n = 1) than expected (n = 10). Mothers of Surinam descent more frequently reported a child with a musculoskeletal anomaly. Older mothers were more likely to report congenital anomalies. No significant trends regarding other risk factors were observed. CONCLUSIONS: No significant trends regarding ethnicity and congenital anomalies were detected. The interpretation of the other results was hampered by methodological differences between the ABCD study and Eurocat. Nationwide registration with active case detection of congenital anomalies is therefore recommended.