Objective To clarify the value of endotoxin concentrations in expressed prostatic secretions (EPS) in the diagnosis and classification of chronic prostatitis. Patients, subjects and methods The study included 88 consecutive patients with chronic prostatitis and 15 controls with no urological disease. The diagnosis and classification were based on a history, symptoms, a digital rectal examination of the prostate, and a white blood cell count in the EPS. Endotoxin concentrations in the EPS or urine were measured using a colorimetric assay and standard microbiological methods used to identify bacterial growth. Results In men with chronic prostatitis caused by Gramnegative or combined Gram-negative and -positive bacteria, the endotoxin levels in urine collected immediately after prostatic massage were significantly greater (P<0.01) than in a midstream urine sample, and the concentration in the EPS was significantly higher (P<0.05) than that in the control group. The same was true of patients with chronic prostatitis and Gram-positive bacteria isolated from the EPS or urine after massage. In patients with chronic pelvic pain syndrome (grade IIIA) the endotoxin level in the urine after massage was also significantly higher (P<0.05) than that of the midstream sample, but there was no significant difference between the concentration in these samples in patients with grade IIIB, and no significant difference between the endotoxin concentration of the EPS in patients with grade IIIB and that in controls. Conclusion Endotoxin concentrations are increased in the EPS or urine (after prostatic massage) of men with bacterial chronic prostatitis or chronic pelvic pain syndrome grade IIIA. The current routine examinations (including bacterial culture and routine examination of EPS or urine) before diagnosis and classifition of chronic prostatitis are insuficient to describe the cause and pathogenesis of this condition. The endotoxin concentration of the EPS or urine after massage may provide a supplementary tool to identify the cause of chronic prostatitis.