Hashimoto‟s thyroiditis is a common autoimmune thyroid disorder mostly seen in middle aged women. Surprisingly little is known about its etiopathogenesis. Usually patients present with hypothyroidism and/or goiter. It is the interaction between genetic/epigenetic and various environmental triggers including iodine deficiency and infections. Several loci have been associated with Hashimoto‟s disease, such as HLA-DR, immune-regulatory genes (CD40, CTLA-4, PTPN22, FOXP3 and CD25) and thyroid-specific genes. HLA-DRb1 Tyr26, Gln70, Lys71 and Arg74 may cause structural changes in pocket 4 and therefore influence binding of certain thyroid derived pathogenic peptides. It seems to be associated with various autoimmune disorders and cancers like papillary thyroid carcinoma and malignant lymphoma.