Little is known about chlamydia survival in the presence of fluoroquinolones in patients with chronic prostatitis syndrome (CPS). In vitro activities of four fluoroquinolones, azithromycin and doxycycline against C. trachomatis in patients with CPS being not treated with antibiotics earlier were investigated and compared. Chlamydia survival in 304 patients with CPS being not treated with antibiotics earlier was analysed and compared. Infection by C. trachomatis was determined in the urethra and expressed prostatic secretion by cell culture test. Azithromycin and ofloxacin were found to be the most active antichlamydial agent with ciprofloxacin and doxycycline being least active. Ofloxacin can be recommended as the primary drug in the treatment of chlamydia-infected patients with CPS. The decision on the prescription of other fluoroquinolones should be made individually. The investigation of chlamydia survival in the presence of antibiotics in patients with CPS and C. trachomatis prior to treatment is recommended.