In only approximately 10% of men with symptoms of chronic prostatitis/chronic pelvic pain syndrome bacterial infection of the prostate can be demonstrated by the Meares and Stamey 4-glass or the pre- and post-prostate massage (PPM) two-glass test. Chronic bacterial prostatitis is mainly caused by Gram-negative uropathogens. The role of Gram-positives, atypicals and anaerobes is still debatable. For treatment, fluoroquinolones are considered the drugs of choice because of their favourable pharmacokinetic properties and their antimicrobial spectrum. As relapse and re-infection are a major problem in chronic bacterial prostatitis, only the results of studies with a follow up period of at least 6 months are meaningful. Analysing the concentrations of various fluoroquinolones in prostatic and seminal fluid as well as in prostatic tissue, it becomes, however, obvious that fluoroquinolones differ not only in plasma concentrations, but also in their penetration ability to these sites. Nevertheless, the concentrations at the site of infection of most fluoroquinolones with this indication should be sufficient for the treatment of chronic bacterial prostatitis caused by susceptible pathogens. On the other hand, male accessory gland infection has been linked to male infertility. However, there is still a lack of evidence showing that bacterial prostatitis would have a negative impact on sperm quality.