AbstractIntroductionThe number of persons with gender incongruence referred to health care is increasing, but national data on the incidence of gender incongruence are lacking. The aim of this study was to quantify the development in number of individuals with gender incongruence over time and to estimate the national incidence in Denmark.Material and methodsHistorical descriptive cohort study. Individuals older than 18 years with legal sex‐change in their person registration number were achieved from Statistics Denmark, and the National Health Register provided data on contact diagnoses related to gender‐identity conditions. By combining these two data sources, we made estimates on incidence and incidence rates for individuals with gender incongruence in Denmark through a 41‐year period 1980–2020.ResultsThrough 1980–2020, the annual number of legal sex‐changes increased in individuals assigned female at birth from 5 to approximately 170 and among individuals assigned male at birth from 10 to approximately 150. The cumulative number of legal sex‐changes at the end of 2019 was 1275 assigned female at birth and 1422 assigned male at birth and 66% of the legal sex‐changes were in individuals below 30 years. Correspondingly, the annual number of contacts with the healthcare system due for gender‐identity‐related conditions increased from 30 during 1990–1999 to around 500 in 2017 (both genders combined), with a 10‐fold increase from 2010 to 2017.ConclusionsThe number of legal sex‐changes and healthcare contacts due to gender‐identity‐related diagnoses increased substantially over the last 40 years with a more than 10‐fold increase during the last decade. This calls for research on possible explanations for this increase, for research on the short‐term and long‐term health consequences of hormonal and surgical treatment regimens and for ensuring adequate healthcare facilities.