We have examined the T cell specificity of a Lewis rat T cell line (R208) specific for a pathogenic, 123 residue cyanogen bromide produced peptide of bovine S-antigen by using two independent sets of overlapping synthetic peptides representing the entire length of the 123 residue fragment. S-antigen, a 48 kDa immunopathogenic photoreceptor cell autoantigen induces T cell mediated experimental autoimmune uveoretinitis (EAU) in experimental animals. Extensive analyses revealed a heterogenous response by the R208 line to the panel of synthetic peptides, proliferating weakly to 4 distinct sites. Unexpectedly, peptides representing sequences (residues 286 - 297 and 303 - 320 of bovine S-antigen) known to actively induce the autoimmune pathology were unable to significantly stimulate the R208 line as assessed by proliferation assays. Similarly, attempts to isolate T cells specific for these sequences from the R208 line have proven unsuccessful. However, two sequences, residues 253 - 269 and 273-289, sufficiently stimulated R208 cells to allow isolation of sub-lines, R208:26 and R208:28, respectively. Neither of these peptides actively induce an autoimmune response. R208:26 does not transfer EAU and R208:28 transfers moderate EAU. As a control, we are able to isolate a pathogenic T cell line (R502) specific for the actively pathogenic sequence, residues 303-320, when this peptide is used as the immunogen. However, the R502 line proliferates to peptides (e.g. 305-322) which do not contain residues 303 and 304 which are critical for the active induction of disease. These results show a multiplicity of distinct T cell epitopes within a relatively small region of S-antigen. Furthermore, there appears to be a dissociation between proliferative sites and pathogenic sites. A partial amino acid sequence (through the 123 residue region) of rat retinal S-antigen predicted from cDNA clone RT.A11 is also reported to show sequence disparities in the region.