To investigate bacterial infection in the seminal vesicles by bacteriological examination and radionuclide imaging in men with chronic prostatitis. The study included 50 patients with chronic prostatitis who showed hot uptake in seminal vesicles on Tc-99m ciprofloxacin imaging and eight patients who did not show hot uptake. The evaluation included the National Institutes of Health Chronic Prostatitis Symptom Index and four-glass test. In all participants, transperineal aspiration of seminal vesicle fluid under the guidance of transrectal ultrasonography and bacteriological examination was carried out. Of the 50 patients who showed hot uptake in the seminal vesicles on the isotope study, microorganisms were isolated from the seminal vesicle fluid in 17 patients (positive predictive value, 34%). The most common causative organisms were Escherichia coli in 13 patients (26%), followed by coagulase-negative Staphylococcus species in two patients (4%), Enterococcus faecalis in one patient (2%) and Chlamydia trachomatis in one patient (2%). No microorganisms were isolated in the eight patients who did not show hot uptake in the seminal vesicles (negative predictive value, 100%). However, there were no significant differences in National Institutes of Health Chronic Prostatitis Symptom Index total scores and subscores between the study groups. Chronic bacterial seminal vesiculitis might simultaneously affect a considerable portion of patients with chronic prostatitis, although the clinical implication of the disease remains to be further investigated.