Chronic bacterial prostatitis (CBP) is a rare infection of the prostate with Escherichia coli being the predominant causative pathogen. Appropriate antimicrobial therapy is mandatory for cure. We report on our experience with a 4-week regimen of ciprofloxacin in 40 men suffering from CBP due to E. coli. Follow-up was conducted over a period of 12 to 24 months. The microbiological work-up included an analysis of expressed prostatic secretions (EPS) and semen. Eradication of the pathogen in EPS was achieved in 92% of patients 3 months after therapy and in about 70 to 80% of patients evaluated 12 and 24 months after treatment, respectively. Treatment failure was not associated with the presence of prostatic calculi, as assessed by transrectal ultrasonography. After successful therapy, mean EPS pH decreased significantly from 7.95 to 7.35. Significant bacteriospermia with E. coli was detected in 21/22 (95.5%) patients before treatment and in 6/22 (27.3%) patients 6 months after therapy. Our data reconfirm ciprofloxacin as an excellent antimicrobial agent in the therapy of CBP. However, eradication of the pathogen is unpredictable and cannot be achieved in every case. Further studies should correlate microbiological treatment success with symptomatic relief, as assessed by standardised questionnaires.