This article discusses the classic autoimmune diseases: pemphigus vulgaris, mucosal pemphigoid, and oral lichen planus. These are generally considered of autoimmune origin or, at a minimum, immune system mediated. Cause, diagnosis, and treatment are discussed. As management of these diseases progresses, continued advances in molecular pathogenesis will allow insight into which strategies can be employed in interfering with the complex cascade of events leading to mucosal impairment and clinical morbidity.