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.