We report a case of Chlamydia-associated arthritis in a 40-year-old man. The patient experienced four episodes of Chlamydia trachomatis urtethritis within a few years. During the present episode, polyarthritis developed a few days after Chlamydia trachomatis urethritis was noted. The patient was diagnosed as having Chlamydia-associated arthritis. Loxoprofen sodium and azithromycin were started. Antibiotics induced clinical improvement of urethritis, although arthritis persisted for 3 months. HLA-B27 was negative, but both HLA-B35 and B40 were positive. Thus, we speculate that positivity for both HLA-B35 and HLA-B40 contributed to the persistence of arthritis in this case. During the course, the levels of Th1, Th17 and regulatory T cells in the peripheral blood were increased on flowcytometry. Thus, we speculate that Th17 may play, at least in part, an important role of the pathogenesis in this case.