Chlamydia trachomatis infections are among the most common sexually transmitted diseases in the world and it is only logical to hypothesize that it alone or in association with mycoplasmas can participate in the initiation and persistence of upper urinary tract infections. Having in mind the inconclusive evidence regarding the role of C. trachomatis in upper urinary tract infections we decided to study the presence of C. trachomatis in the upper urinary tract of patients with obstructive pyelonephritis using the polymerase chain reaction. We studied 20 patients (12 female and 8 male, aged 20-60 years) with symptoms and signs of acute pyelonephritis in accordance with Kunin's criteria (1997). Samples were taken during surgery of the upper urinary tract by aspirating urine from the renal pelvis or the ureter above the level of the obstruction and analyzed for the presence of bacterial pathogens using routine microbiological techniques and employing the "AMPLICOR CT/NG" test (Roche Diagnostic Systems, Branchburg, NJ, USA) for the presence of C. trachomatis. Chlamydia trachomatis was found in the aspirated urine of 5 patients (25%). In 3 of the patients the microbiological tests of the aspirated urine did not establish any other microbial agent. In the other two Escherichia coli and Proteus mirabilis were cultured. The analysis of the clinical and laboratory findings in the patients with Chlamydia trachomatis infection alone and those with an associated bacterial pathogen failed to reach statistical significance. Following the operation all of the patients received treatment with Ofloxacin 200 mg bid for 7 days with a favorable clinical and laboratory outcome. In our opinion, the AMPLICOR CT/NG test is a sensitive and specific method for diagnosing low-number Chlamydia trachomatis infections of the upper urinary tract in patients with obstructive pyelonephritis. Chlamydia trachomatis should be considered as a possible etiologic agent in acute pyelonephritis and the therapeutic regimen in such patients should be targeted at its possible underlying presence.