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Anne Broe,1,2 Per Damkier,1,2 Anton Pottegård,3 Jesper Hallas,1,3 Mette Bliddal3,4 1Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark; 2Department of Clinical Research, University of Southern Denmark, Odense, Denmark; 3Department of Clinical Pharmacology, Pharmacy, and Environmental Medicine, University of Southern Denmark, Odense, Denmark; 4Department of Clinical Research, Open Patient Data Explorative Network, University of Southern Denmark and Odense University Hospital, Odense, DenmarkCorrespondence: Anne BroeDepartment of Clinical Biochemistry & Pharmacology, Odense University Hospital, JB Winsløwsvej 19, 2, Odense 5000 Odense C, DenmarkEmail anbroe@health.sdu.dkBackground: Danish health registers are used widely to examine associations between specific risk factors and congenital malformations. Various overall prevalence rates of malformations have been reported in Denmark indicating differences in the underlying data sources or malformation definitions. We described trends in registration of malformations in Denmark 1997– 2017 and identified potential caveats for the use of Danish health registries in epidemiological studies. We composed a Danish adaptation of EUROCATs definition of malformations.Methods: Using nationwide Danish health registries, we identified all recorded pregnancies and followed livebirths for up to 5 years. We described the different data sources, ways to identify malformations, the overall rate of malformations over time, and identified the 10 most common major malformations.Results: A total of 1,340,774 foetuses and infants from 1,313,281 pregnancies among 747,144 women from 1997 to 2017 were analysed. Using primary and secondary diagnoses from all available sources and restricting hip malformations to diagnoses after 6 weeks postpartum, we found that 65,411 (49/1000) foetuses or infants had at least one major malformation defined by our Danish translation of EUROCATs definition of malformations. The prevalence of major malformations increased over time from 39/1000 in 1997 to 53/1000 in 2017. The most common specific malformations were malformations of cardiac septa (Q21) and great arteries (Q25) with a peak of 10 and 6/1000 births in 2010 and 2009, respectively.Conclusion: Malformations should be identified using primary and secondary diagnoses from the Birth register, the Patient register, and the Cause of Death register. To increase transparency and external validity, classification of major malformations should be based on the Danish adaptation of EUROCATs classification of malformations.Keywords: malformations, anomalies, health registries, epidemiology, EUROCAT