The association between MHC polymorphisms and autoimmune thyroid disease has been complicated by the observation of MHC class II antigen expression by the human thyroid gland. It is possible that the MHC associations observed in animal and human population studies may have mechanistic explanations at the level of the thyroid cell. There is evidence for expression of HLA-DR allospecific antigen in both normal and abnormal human thyroid cells, with enhanced expression in patients with autoimmune thyroid disease. Such MHC class II expression appears to be mediated primarily by lymphokine secretion from intrathyroidal T lymphocytes. Thyroid cell HLA-DR antigen participates in activation and amplification of T cells and is likely to be involved in presentation of thyroid antigen to the immune system. The relationship between these immune interactions and the initial events leading to the development of autoimmune thyroid disease remains to be understood.