Antimicrobial treatment is usually used for chronic prostatitis. However, the efficacy of such treatment has not been fully evaluated. We conducted a study to evaluate the efficacy of gatifloxacin for patients with chronic prostatitis using the Japanese version of the National Institutes of Health Chronic Prostatitis Symptom Index (JPN-NIH CPSI). The study included 46 patients for final analysis. Patients who were younger than 65 years of age were treated with 200 mg gatifloxacin twice daily, and those who were 65 years and older were treated with 100 mg gatifloxacin twice daily, for 4-8 weeks. The study consisted of 10 patients in category II, 13 in category IIIA, 11 in category IIIB, and 12 who were unclassified. The gatifloxacin treatment resulted in significant reductions in the scores on the JPN-NIH CPSI. Of the total number of patients, 58.1% and 27.9% were 25% and 50% responders, respectively, 4 weeks after treatment, and these figures improved to 66.7% and 33.3%, respectively, 8 weeks after treatment. No significant difference was found in the changes in symptom scores between Category II and Category IIIA/IIIB groups. In conclusion, gatifloxacin treatment improved the symptoms in patients with chronic bacterial and nonbacterial prostatitis. This study is the first in this country to evaluate the efficacy of antimicrobial treatment for chronic prostatitis by using the NIH CPSI.