Objective: The aim of our study was to investigate the coexistence of autoimmune diseases (autoimmune thyroid disease and type 1 diabetes mellitus, T1DM) in patients affected by Juvenile Chronic Arthritis (JCA)., Methods: We studied 66 patients affected by JCA, 42 females and 24 males: 42/66 patients had a pauciarticular form of JCA, 13/66 had a polyarticular form and 11/66 had a systemic form. All the patients underwent autoimmune thyroid screening through determination of anti-thyroglobulin (TgA) and anti-peroxidase (TPOA) autoantibodies. Patients with TgA and/ or TPOA, underwent thyroid sonography. T1DM screening included determination of anti-glutamic acid decarboxylase (GADA), anti-insulin (IAA), anti-tyrosine phosphatase-like protein (IA-2A) and anti-islet cell (ICA) autoantibodies. Oral glucose tolerance test (OGTT) was performed only in patients with autoantibody positive values. HLA typing for risk of T1DM was performed in 43 patients., Results: Nine female patients (14%) showed anti-thyroid autoantibodies, in particular: TgA in 3 cases, TPOA in 5, TgA and TPOA in only 1. In 3 of these patients, ultrasound examinations showed thyroid abnormal pattern, suggesting Hashimoto's thyroiditis. As regards T1DM, only 2 patients showed positive levels of GADA. As regards HLA typing, one or more T1DM susceptibility heterodimers were detected in 20 patients (46%) (13 with 1 heterodimer, 7 with 2 heterodimers)., Conclusion: Our study showed that anti-thyroid autoantibody frequency (9/66, 14%) was higher in JCA than in the general population, while T1DM markers (islet autoantibodies and genetic markers) were not frequent. These results suggest to investigate specific markers of thyroid autoimmunity in patients with JCA, in particular in females with JCA pauciarticular form.