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Background: The incidences of both paediatric obesity and autoimmune diseases have been increasing, but their relationship with one another is unclear., Objective: To determine whether obesity or particular dietary patterns in school-aged children are potential risk factors for autoimmune diseases during adolescence., Methods: This matched case-control study included 525 children, followed up from a median age of 11.3 to 16.7 years. Of them, 105 children received primary autoimmune diagnoses (diabetes, thyroiditis, arthritis, or inflammatory bowel diseases) after baseline and generated the case group. Four children with matching age, sex, and residential area generated the control group of 420 children. At baseline, age- and sex-specific body mass index categories were acquired and waist-to-height ratio (WHTR) was calculated. Central obesity was present when WHTR ≥0.5. Dietary patterns were analysed using a food frequency questionnaire (FFQ)., Results: School-aged children with central obesity were 2.11 (OR, 95% CI 1.11-3.98) times more likely to develop autoimmune diseases before age of 19 years than those without central obesity. Being overweight was not related to the onset of these diseases (OR 1.60, 95% CI 0.89-2.87, nor were dietary patterns., Conclusion: Central obesity in school-aged children was related to the development of autoimmune diseases, while being overweight and dietary patterns were not., (© 2021 The Authors. Pediatric Obesity published by John Wiley & Sons Ltd on behalf of World Obesity Federation.)