BACKGROUND: There is little known about the association of Kawasaki disease with autoimmune diseases. This 12-year follow-up study determined the risk for an autoimmune disease in children who had Kawasaki disease. METHODS: All individuals born in South Korea between 2002 and 2005 were identified using the National Health Insurance Service's (NHIS) database. Incidence density sampling was used to identify 16,398 patients in the exposed cohort (diagnosis of Kawasaki disease between 2002 and 2005) and 163,980 matched (1:10) children in the unexposed cohort. Participants were followed from the date of diagnosis of Kawasaki disease (index date) until the first diagnosis of an autoimmune disease, death, or end of the study (December 31, 2017). Diagnoses of autoimmune diseases were according to ICD-10 codes. FINDINGS: The median age at the index date was 2.2 years (interquartile range: 1.1-3.7). During follow-up, 1139 children had newly diagnosed autoimmune diseases in the exposed cohort (incidence rate: 59.3 per 10,000 person-years) and 9752 children had newly diagnosed autoimmune disease in the unexposed cohort (incidence rate: 50.4 per 10,000 person-years), corresponding to an absolute difference of 8.9/10,000 person years (95 % CI: 5.3-12.5). Kawasaki disease was also associated with multiple individual autoimmune diseases: juvenile idiopathic arthritis (HR=1.27), Henoch-Schönlein purpura (HR=1.21), polymyositis/dermatomyositis (HR=2.12), vitiligo (HR=1.17), idiopathic thrombocytopenic purpura (HR=2.30), and acute rheumatic fever and chorea (HR=3.35). INTERPRETATION: Korean children with Kawasaki disease had an increased risk of autoimmune disease during a 12-year follow-up period. These findings suggest a biological relationship between Kawasaki disease and subsequent autoimmune disease.