All infants and children born alive with documented congenital heart disease (excluding those weighing less than 2500 g at birth with a diagnosis of patent arterial duct) within the county of Merseyside between 1979 and 1988 were identified from the combined records of the Liverpool Congenital Malformations Registry and the Cardiac Unit, Royal Liverpool Children‘s Hospital Alder Hey, Liverpool. In total, 1543 cases were disclosed from a live-birth population of 203,880 providing a prevalence rate at birth of 7.57 (95% confidence interval: 7.20–7.96) cases per 1000 livebirths. The overall crude death rate was 18.5% (95% confidence interval: 16.4–20.3). An additional 240 (15.6% [95% confidence interval: 13.8–17.5%]) cases of heart disease not identified by the registry were disclosed from the records of the cardiac unit, demonstrating the unreliability of rates published by monitoring bodies. The annual prevalence rate at birth varied from 6.3 to 9.0 per 1000 livebirths, and seemed to be associated with the impact of new imaging technology. Regional variation was marked (5.3 to 8.9 per 1000 livebirths) and unaccountable in terms of potential morphogenetic mechanism, suggesting inconsistencies in referral of cases. Exclusion of regions of poor ascertainment in the calculation of a revised figure for the prevalence rate at birth suggests that as many as 89 in every 10,000 infants born alive may have structural cardiac anomalies. In conclusion, annual and regional variation of ascertainment in registry studies remains the enemy of an accurate description of the true prevalence rate at birth for congenital heart disease.