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Objective To determine the prevalence and clinical characteristics of juvenile idiopathic arthritis (JIA) in Alaska Native children. Methods Potential cases of JIA were identified by querying administrative data from hospitals and clinics in the Alaska Tribal Health System for codes possibly identifying JIA. Medical record abstraction was performed to confirm criteria met for JIA, demographic and clinical characteristics, and treatment patterns. Individuals age ≤18 years with a confirmed diagnosis of JIA were included. The denominator for prevalence was the 2015 Alaska Area Indian Health Service user population age of ≤18 years. Results The unadjusted prevalence of JIA in Alaska Native children was 74.6 per 100,000 (age-adjusted 79.0 per 100,000). JIA was more common in females than males (unadjusted prevalence 105.8 versus 45.0 per 100,000). Oligoarthritis was the most common subtype (31% of cases), but polyarthritis and enthesitis-related arthritis were also common (26% and 24% of cases, respectively), with a notably high prevalence of enthesitis-related arthritis. The median age at diagnosis was 9 years. Of the combined cohort with results available, 56% were antinuclear antibody positive, 23% were rheumatoid factor positive, 19% were anti-cyclic citrullinated peptide antibody positive, and 57% had the presence of HLA-B27. Uveitis had been diagnosed in 16% of cases. Conclusion The prevalence of JIA in Alaska Native children may be higher than the general US population. Enthesitis-related arthritis makes up a higher proportion of cases than in other populations described likely because of the high prevalence of HLA-B27 in this population.