Juvenile idiopathic arthritis (JIA) is the most frequent disease of the connective tissue in childhood. JIA is divided into 7 clinical subtypes. This article describes the first epidemiological population- and hospital-based investigation in the field of JIA in Estonia. In the years 1998–2000 the mean annual incidence rate of JIA was 21.7 per 100 000 children aged 0–15 years. During the investigation period the incidence rate rose fourfold, probably due to environmental factors and an increase in awareness among family doctors.