Autoimmune diseases, including autoimmune thyroid diseases (AITD), affect women more often than men. AITD, namely Hashimoto’s thyroiditis (HT) and Graves’ disease, are the most common autoimmune endocrine diseases in women of reproductive age. Over the last few decades, patients with an AITD have been younger and autoantibodies were less frequent despite typical histological changes of AID. The female predominance is thought to be due to hormonal, genetic, and environmental factors that regulate the innate and adaptive immune system. Estrogens induce type 2 cytokines, stimulating mainly CD4+ cells and antibody production, whereas androgens induce type 1 cytokines, stimulating CD8+ cells. The genetic background of gene activation and deactivation is considered a crucial mechanism in the development of AITD.