Background: The diagnosis of tuberculous peritonitis (TP) may be difficult and elusive. The present study was designed to demonstrate the diagnostic usefulness of a nested polymerase chain reaction (PCR) assay, specific for the IS6110 insertion element of M. tuberculosis complex, in patients with ascites who were suspected of having TP in order to achieve a more timely diagnosis and treatment. Methods: Three HIV-negative patients suffering from fever and ascites were evaluated for suspected TP. Specimens were obtained from ascitic fluid, bone marrow, and peripheral blood and analyzed by both conventional methods and nested PCR for the presence of bacilli. Response to antituberculous treatment was considered as the final criterion for diagnosis of peritoneal tuberculosis. Results: All three patients had an excellent response to antituberculous therapy. Our PCR-based protocol detected M. tuberculosis complex DNA in the ascitic fluid of all patients, whereas conventional methods failed to establish the disease. Furthermore, in one patient, M. tuberculosis was also detected in both bone marrow and peripheral blood. Conclusions: PCR amplification of the IS6110 sequence of M. tuberculosis complex in ascitic fluid is a useful tool when peritoneal tuberculosis is suspected. However, its validity still needs to be established.