The location of the monoclonal antibody, MAbA9-C6, binding site and two uveitopathogenic sites in S-antigen have been determined. Using cyanogen bromide, S-antigen was cleaved into nine peptides, designated C1 to C9. MAbA9-C6 bound selectively to one large peptide designated C5, consisting of 122 amino acids. Six peptides (20 to 22 amino acids in length) designated 2,3,K,L,N and M, corresponding to the entire length of peptide C5, were synthesized chemically. In a radioimmunoassay and a dot-binding immunoassay, MAbA9-C6 bound selectively to one of the six peptides, peptide 3, indicating that this region of peptide C5 contains the MAbA9-C6 binding site. Twelve smaller peptides (ten amino acids in length), corresponding to the amino acid sequence of peptide 3, were synthesized and used in a competitive inhibition binding assay. These studies localized the MAbA9-C6 binding site to a small region within peptide 3. In addition, peptide K and peptide M were highly pathogenic for the induction of experimental auto-immune uveitis (EAU). Clinical and histological evidence of a severe uveo-retinitis, indistinguishable from that seen with native S-antigen, was documented in Lewis rats immunized with the synthetic peptides (50 micrograms), 11-12 days following immunization. Our results show that the MAbA9-C6 binding site and the two uveitopathogenic sites lie in close proximity to each other within the region of S-antigen corresponding to peptide C5. Furthermore, microcomputer analysis of the average hydrophilicity/hydrophobicity values of the amino acid sequence corresponding to peptide C5 shows that the MAbA9-C6 binding site and one uveitopathogenic site (peptide K) lie on the adjacent peaks. The significance of these findings and their relationship to the role of S-antigen in the pathogenesis of EAU and the phototransduction of vision is discussed.