Clinical autoimmunity requires both activation of self-reactive T cells as well as a failure of peripheral tolerance mechanisms. We previously identified one such mechanism that involves regulatory T cells recognizing TCR Vβ8. 2 chain-derived peptides in the context of MHC. How this regulation affects the fate of target Vβ8. 2+ T lymphocytes in vivo that mediate experimental autoimmune encephalomyelitis has remained unknown. The present study using immunoscope and CFSE-labeling analysis demonstrates that the expansion of regulatory CD4 and CD8 T cells in vivo results in apoptotic depletion of the dominant, myelin basic protein-reactive Vβ8. 2+ T cells, but not subdominant Vβ13+ T cells. The elimination of only activated T cells by this negative feedback mechanism preserves the remainder of the naive Vβ8. 2+ T cell repertoire and at the same time results in protection from disease. These studies are the first in clearly elucidating the fate of myelin basic protein-specific encephalitogenic T cells in vivo following regulation.