This study aimed to investigate the clinical characteristics, treatment, and prognosis of juvenile idiopathic inflammatory myopathies (JIIM) in Japan for each myositis-specific autoantibody (MSA) profile.A multicenter, retrospective study was conducted using data of patients with JIIM at nine pediatric rheumatology centers in Japan. Patients with MSA profiles, determined by immunoprecipitation using stored serum from the active stage, were included.MSA were detected in 85 of 96 cases eligible for the analyses. Over 90% of the patients in this study had one of the following three MSA types: anti-MDA5 (n = 31), anti-TIF1γ (n = 25), and anti-NXP2 (n = 25) antibodies. Gottron papules and periungual capillary abnormalities were the most common signs of every MSA group in the initial phase. The presence of interstitial lung disease (ILD) was the highest risk factor for patients with anti-MDA5 antibodies. Most patients were administered multiple drug therapies: glucocorticoids and methotrexate were administered to patients with anti-TIF1γ or anti-NXP2 antibodies. Half of the patients with anti-MDA5 antibodies received more than three medications including intravenous cyclophosphamide, especially patients with ILD. Patients with anti-MDA5 antibodies were more likely to achieve drug-free remission (29% vs 21%) and less likely to relapse (26% vs 44%) than others.Anti-MDA5 antibodies are the most common MSA type in Japan, and patients with this antibody are characterized by ILD at onset, multiple medications including intravenous cyclophosphamide, drug-free remission, and a lower frequency of relapse. New therapeutic strategies are required for other MSA types.