Previous analyses of T cell recognition sites on immunopathogenic neural autoantigens have demonstrated, using LEW rats, the functional dissociation of in vitro proliferative responses and the ability to actively induce autoimmune diseases. In experimental autoimmune uveoretinitis, immunization of LEW rats with bovine retinal S-Ag reveals the presence of three immunodominant T cell recognition sites located in regions containing sequence differences between bovine and rat S-Ag. Immune responses of LEW rats to self (rat) and nonself (bovine and human) peptide homologues representing these three sites were compared. The immunodominant sequences of heterologous S-Ag were found to predict new pathogenic T cell recognition sites in the corresponding autologous rat sequence. Furthermore, in vitro proliferative responses to the pathogenic autologous sequences are dramatically diminished relative to the responses of lymphocytes raised to the non-self homologues. A pathogenic T cell line, R858, efficiently transferred disease, but was unresponsive to the autologous S-Ag peptide in proliferation assays. However, responses to autologous peptides were readily detected using nonirradiated splenic APC. Detection of responses to non-self peptides was independent of this radiosensitive Ag-presenting activity. The lack of in vitro proliferative responses to pathogenic autologous sequences by T cells bearing self-specific receptors, contrasted with the strong proliferation induced by non-self peptide homologues, suggests a mechanism of unresponsiveness to self.