To investigate the role of cytochrome P450 1A1 (CYP1A1) and manganese superoxide dismutase (Mn SOD) genes polymorphisms in the susceptibility to reactive arthritis, the polymorphisms of CYP1A1 and Mn SOD genes were determined in 43 patients with reactive arthritis following Chlamydia trachomatis infection and 92 healthy controls by polymerase chain reaction (PCR)/restriction fragment length polymorphisms (RFLP) method. The frequencies of CYP1A1 4887C/A and C/A+A/A were significantly higher in patients with reactive arthritis than in controls. Moreover, the increased frequency of CYP1A1 4887A in patients with reactive arthritis is independent of HLA-B27. The frequency of Mn SOD 1183T/T tended to be increased in patients with reactive arthritis. We also found that the frequency of CYP1A1 4887A was significantly increased in Mn SOD 1183T/T(+) reactive arthritis patients compared with 1183T/T(+) controls. CYP1A1 4887A may be a risk factor for the development of reactive arthritis, especially in the presence of Mn SOD 1183T/T.