We have used transgenic mouse models to examine the mechanisms of tolerance in CD4(+) T lymphocytes to soluble, systemic and cell-associated, tissue-restricted self-antigens. Anergy to an islet antigen, as a model of a tissue antigen, is dependent on the inhibitory receptor cytotoxic T-lymphocyte antigen-4 (CTLA-4), and tissue-restricted autoimmunity is inhibited by regulatory T lymphocytes. Anergy to a circulating systemic antigen can occur independently of CTLA-4 signals, and it is induced primarily by a block in proximal receptor-initiated signals. CD4(+)CD25(+) regulatory T cells are generated in response to both forms of self-antigens, but the induction is much more efficient with the tissue antigen. Receptor desensitization can be induced by the systemic antigen even in the absence of regulatory T cells, but tolerance can be broken by immunization much more easily if these cells are absent. Deletion of mature T cells is striking with the systemic antigen; there is little evidence to support peripheral deletion as a mechanism of tolerance to the tissue antigen. Thus, both distinct and overlapping mechanisms account for unresponsiveness to different forms of self-antigens. These results establish a foundation for searching for genetic influences and pathogenic mechanisms in organ-specific and systemic autoimmune diseases.