Objectives: To investigate the prevalence and patterns of anti-nuclear antibodies (ANA) in different subtypes of juvenile idiopathic arthritis (JIA) according to the International League of Associations for Rheumatology (ILAR) criteria. Methods: One hundred and fifty-three Korean patients (M:F 83:70) with JIA were followed between 1990 and 2006 and were tested for ANA by an indirect immunofluorescence method using HEp-2 cells as the substrate. ANA tests were repeated in 37 patients during the course of the disease. The median age at onset was 7.5 years (range 0.8-15.9 years). Results: ANA were positive in 50 (33%) of the 153 patients at a dilution of 1:40 or higher (>1:40 in 70%, >1:80 in 2%, >1:160 in 16%, >1:320 in 2%, and >1:640 in 10%). The patterns of immunofluorescence staining were homogeneous in 50%, speckled in 38%, nucleolar in 8%, and centromere in 4%. ANA titres were decreased in 25 (68%) of the 37 patients, and the nuclear fluorescence patterns changed in 14 (38%) during follow-up. ANA seropositivity was associated with female sex (p<0.0001), negative HLA-B27 (p = 0.01), and a persistently elevated erythrocyte sedimentation rate (ESR) at follow-up (p = 0.014). Furthermore, a high ANA titre (>1:160) was associated with a poor clinical outcome (active patients at follow-up) (p = 0.005). Conclusions: ANA may be an important marker of disease activity in patients with JIA. ANA titres tend to decrease during disease remission but the fluorescence patterns do not appear to be related to disease activity or clinical outcome.