Environmental factors can play an important role in the development of autoimmune thyroiditis (AT) and other autoimmune diseases. This article reviews the role of heavy metals and infectious agents in AT. Memory T lymphocytes can be used as biomarkers of susceptibility to mercury and other inflammation triggers in individual patients. If metal allergy is found, the patient should avoid all exposure to the allergenic substance. Mercury-allergic patients may benefit from replacement of dental amalgam.