Autoimmune thyroid diseases, including Hashimoto's thyroiditis and Graves' disease, are the most common causes of acquired thyroid dysfunction in children and adolescents. They are often diagnosed at puberty, with a female predominance. A familial predisposition and associations with other autoimmune diseases such as celiac disease and type 1 diabetes point to underlying genetic mechanisms. This predisposition is attributed to the polymorphism of multiple HLA (Human Leukocyte Antigen) and non-HLA susceptibility genes, opening the field for the development of targeted therapies that can potentially modify the course and prognosis of autoimmune thyroid diseases.