Findings could not corroborate a specific correlation between juvenile idiopathic arthritis (JIA) and other autoimmune phenomena. Interpretation is challenging due to the lack of well-matched control groups. Further data required to confirm the suspected elevated risk of developing other autoimmune phenomena in JIA patients.

• In Germany, autoantibodies prevalence in JIA patients remains unknown.

• This analysis involved 499 patients in the prospective, multicenter inception cohort of children newly diagnosed with JIA (ICON-JIA) from whom samples were analyzed for the presence of anti-thyroid antibodies, celiac disease-specific antibodies, and connective tissue disease-associated antibodies (CTD-screen).

• Either clinically diagnosed autoimmune comorbidity or elevated autoantibodies was present in 76 (15.2%) patients.

• Clinical autoimmune comorbidity was present in 21 patients; of these, only 8 also had serological positivity at the time of testing, while 55 had autoantibodies without clinical diagnosis.

• Therefore, at least one elevated autoantibody was present in 63 patients (12.6%).

• Of the overall samples analyzed, 3% showed presence of antibodies against thyroglobulin and 4% demonstrated the existence of antibodies against thyreoperoxidase.

• TSH receptor antibodies could not be identified in any of the 499 cases.

• Overall 0.4% of the patients had increased tissue transglutaminase antibodies.

• There was a positive screen for CTD-specific antinuclear antibodies in 7%, but only rarely specific antibodies (anti-dsDNA 1.4%, anti-SS-A and -SS-B 0.2% each, anti-CENP-B 0.4%) were corroborated.