General registration of congenital malformations was established in Denmark in the early 1960s as a consequence of the thalidomide tragedy. The aims of the present paper are to describe the registration of congenital malformations in Denmark since the thalidomide tragedy, to discuss the limitations of these data and to point towards possibilities for improving the registration of congenital malformations in the future. Important components in a surveillance system are compulsory detailed reporting of malformations shortly after the diagnoses have been made and continuous expert evaluation of all reports. However, since 1995 the registration of congenital malformations in Denmark is based mainly on routine discharge diagnoses from hospitals. A high quality registration of congenital malformations in Denmark would be particularly valuable, because such a register together with existing health related registers and an ongoing large scale cohort study of pregnant women would provide a unique resource for etiological research in congenital malformations. Considering the consequences of congenital malformations for the affected children, their families and society, the establishment of a high quality registration of congenital malformations seems justifiable--and the Swedish experience shows that it is feasible.