ABSTRACTBackgroundAlthough accessing administrative data in healthcare databases may be a more time‐efficient and cost‐effective method of conducting surveillance, there is evidence suggesting that administrative data alone are not sufficient for population‐based surveillance of congenital anomalies.ObjectiveTo propose recommendations to maximise the potential use of healthcare databases for surveillance of congenital anomalies based on our data linkage experiences and results from the EUROlinkCAT study.MethodsEUROlinkCAT is a population‐based cohort study of 99,416 children with anomalies born between 1995 and 2014. The congenital anomaly case records of children in 11 European congenital anomaly (EUROCAT) registries (eight countries) were linked to standardised administrative healthcare data (birth records, death records and hospital discharge records) to evaluate mortality and morbidity outcomes in these children. Overall, 97% of children with anomalies were successfully matched to their records in their national or regional administrative databases. Recommendations to improve surveillance of anomalies when using healthcare data were developed through establishing and analysing data from this cohort.ResultsThe primary recommendation is to develop systems to report anomalies diagnosed in foetuses who undergo a termination and link these data to their mothers. Each liveborn baby must be assigned a permanent unique identification number at birth to enable accurate linkage across healthcare databases. Implementing and improving existing algorithms to discriminate between major anomalies and suspected or minor anomalies will improve accuracy in coding. Heterogeneity in coding anomalies will improve by avoiding the use of ‘unspecified’ or ‘other specified’ codes in hospital databases. Relaxation of country‐specific regulations concerning the suppression of small numbers are necessary to enable data to be combined across European countries.ConclusionImplementation of these recommendations will enable the information in electronic healthcare databases, in conjunction with Congenital Anomaly registries, to be fully exploited and hence will improve the surveillance of anomalies in children.