We investigated the seminal micro-flora of 116 men. Eighty-four men had chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS), and 34 of them were also leukocytospermic. Thirty-two asymptomatic men formed the control group. Micro-organisms were found in all of the 116 seminal fluid specimens. More than 20 different micro-organisms were found in both groups. Neisseria gonorrhoeae and Chlamydia trachomatis were not found. A high frequency of anaerobic bacteria was found in all groups (68-79%), and in most of the specimens, anaerobic micro-organisms were equal to or outnumbered the aerobic strains. We found 1-8 different micro-organisms in each semen sample, the total count of micro-organisms ranged from 10(2) to 10(7)/mL of semen. Both parameters were significantly higher in leukocytospermic CP/CPPS (NIH IIIA category) patients (median=5 different micro-organisms; total median count 5 x 10(4)) than in the control group (median=3 different micro-organisms; total median count 10(3)). In the CP/CPPS patients, the prevalence and/or count of some opportunistic bacteria was higher than in the control group. To show that the micro-organisms do not originate from the urethra, first voided urine was also investigated in 17 prostatitis patients and 15 controls. One patient had significantly fewer micro-organisms (median 1 vs. 4) and a lower total count of micro-organisms (median 10(2) vs. 10(4)/mL) in the first-catch urine than in the seminal fluid. We found only one third of the micro-organisms to be similar in urine and semen while anaerobic bacteria and some aerobic opportunists were infrequent in urine. Semen is a suitable specimen for the diagnosis of prostatitis.