Thyroid autoimmune diseases are complex, polygenic afflictions the penetrance of which is heavily dependent on various environmental influences. In their pathogenesis, an afferent stage (enhanced autoantigen presentation), a central stage (excessive expansion and maturation of autoreactive T and B cells), and an efferent stage (effects of autoreactive T cells and B cells on their targets) can be discerned. At each stage, a plethora of inborn, endogenous or exogenous factors is able to elicit the abnormalities characteristic of that stage, thus opening the gateway to thyroid autoimmunity. Iodine is an important exogenous modulating factor of the process. In general, iodine deficiency attenuates, while iodine excess accelerates autoimmune thyroiditis in autoimmune prone individuals. In nonautoimmune prone individuals, the effects of iodine are different. Here iodine deficiency precipitates a mild (physiological) form of thyroid autoimmune reactivity. Iodine excess stimulates thymus development. Iodine probably exerts these effects via interference in the various stages of the autoimmune process. In the afferent and efferent stage, iodine-induced alterations in thyrocyte metabolism and even necrosis most likely play a role. By contrast, in the central phase, iodine has direct effects on thymus development, the development and function of various immune cells (T cells, B cells macrophages and dendritic cells) and the antigenicity of thyroglobulin.