To determine whether there are differences in the immunopathogenesis of different endogenous uveitis syndromes, the phenotypic characteristics of immune cells were analysed among patients with endogenous uveitis. The aetiology of the uveitis included idiopathic recurrent acute anterior uveitis (18 patients), idiopathic intermediate uveitis (13 patients), Behçet's uveitis (17 patients), Vogt-Koyanagi-Harada syndrome (7 patients), and so on. Flow cytometric analysis was performed using immune cells of the aqueous humor and the peripheral blood during the active phase of intraocular inflammation, and monoclonal antibodies to CD3, CD4, CD8, CD14, CD19, CD56, TCR gammadelta, pan TCR alphabeta and Valpha24. CD8+ T cells were predominant in the aqueous humor of the patients with Behçet's uveitis, whereas CD4+ T cells were mainly found in the aqueous humor of patients other than those with Behçet's uveitis. The number of NKT (CD3+CD56+) cells was significantly higher both in the aqueous humor and the peripheral blood of the patients with Behçet's uveitis compared with the other groups (P < 0.05). CD8+CD56+ cells were the predominant subtype of the increased NKT cells in patients with Behçet's uveitis. In addition, intraocular infiltration of CD14+ cells significantly differed among the uveitis patients (P < 0.05). These results suggest that the immunopathogenesis of endogenous uveitis can vary between syndromes, and that CD8+CD56+ NKT cells may play an important role in the immunopathogenesis of Behçet's uveitis.