Background: Allergic and autoimmune diseases are caused by an impaired immunological response resulting from different types of T-helper (Th) cells. Since the Th cell production is in a certain balance, an inverse relationship between the 2 disease groups may exist. In this study, we aimed to investigate the frequency of allergic diseases in children with autoimmune thyroiditis (AT). Methods: Symptoms of allergic diseases were investigated by the (International Study of Asthma and Allergies in Childhood) ISAAC questionnaire. The questionnaire was administered to a group of 300 children with AT and a control group of 300 children with no known autoimmune disease. The risk factors for allergic diseases and sociodemographic characteristics were investigated. A multivariable logistic regression analysis was performed with the risk factors of allergic diseases. Results: Asthma, wheezing during the last year, wheezing with exercise, disease-free night cough, and night cough were significantly less common in patients with AT. Allergic rhinitis symptoms, except physician-diagnosed allergic rhinitis, are found significantly less frequently in patients with AT. It was found that the presence of AT and an increase in the number of children in the family reduce the risk of allergic diseases; cat-dog contact before 1 year of age and the presence of asthma, eczema, or allergic rhinitis in the mother increase the risk of allergic diseases. Conclusions: Asthma and allergic rhinitis symptoms were significantly less common in children with AT. AT reduces the risk of allergic diseases.