Significance In the present study, we provide evidence of a cellular mechanism of breach of tolerance in an in vivo model of spontaneous autoimmune thyroiditis (AIT). We observe that self-antigen (Ag) specific T _reg circulate in all lymphatic tissues except for the lymph nodes (LNs) draining the thyroid, which represents the site of inflammation. By contrast, cognate effector T cells accumulate in the draining LNs and thyroid. The absence of T _reg unleashes cognate T _eff , which promote tissue destruction. We demonstrate that the organ-restricted disappearance of T _reg is driven by the self-Ag, aberrantly expressed in a highly inflammatory environment, by a mechanism of activation-induced cell death.