CD4+ CD25+ regulatory T cells (T(Reg)) play a critical role in the control of autoimmunity. However, little is known about how T(Reg) suppress self-reactive T cells in vivo, thus limiting the development of T(Reg)-based therapy for treating autoimmune diseases. This is in large part due to the dependency on a state of lymphopenia to demonstrate T(Reg)-mediated suppression in vivo and the unknown Ag specificity of T(Reg) in most experimental models. Using a nonlymphopenic model of autoimmune pneumonitis and T(Reg) with known Ag specificity, in this study we demonstrated that these T(Reg) can actively suppress activation of self-reactive T cells and protect mice from fatal autoimmune pneumonitis. The protection required T(Reg) with the same Ag specificity as the self-reactive T cells and depended on IL-10 and TGF-beta. These results suggest that suppression of autoimmunity by T(Reg) in vivo consists of multiple layers of regulation and advocate for a strategy involving Ag-specific T(Reg) for treating organ-specific autoimmunity, because they do not cause generalized immune suppression.