Background Retinal S-antigen (S-Ag) is a most characterized autoantigen of autoimmune uveitis. The recognized immunodominant epitope of human S-Ag in patients with uveitis has not been identified. In this study, we selected certain patients with active uveitis to map the Th1 cell epitope spectrum of human S-Ag in Behcet's disease(BD). Methods Blood samples were taken from eight active BD patients who showed an immune response to 40 mixed overlapping peptides spanning the entire sequence of human S-Ag. Peripheral blood mononuclear cells were isolated and stimulated with single S-Ag peptide at 5 μg/ml or 20 μg/ml. Single-cell immune responses were measured by IFN-γ ELIspot assay. Results BD patients heterogeneously responded to the SAg peptides at two concentrations. In general, the responses to 5 μg/ml peptides were slightly stronger than those to 20 μg/ml peptides, while the maximum SFC frequency to single peptide at the two concentrations was similar. Several peptides including P31, P35 and P40 induced a prominent response, with the frequency of S-Ag specific cells being about 0.007%. Significant reactivity pattern shift was noted in patients with different disease courses. Conclusions Certain active BD patients have S-Ag specific Th1 cells with a low frequency. The S-Ag epitope specificity between patients is highly heterogeneous, and varies with the uveitis course.