Detection of P. carinii has increased with the use of polymerase chain reaction (PCR), particularly in sputum samples. In this study, sputum samples obtained from 30 immunosuppressed patients with respiratory symptoms (12 HIV-infected) were tested by standard cytochemical staining (Giemsa and methenamine silver), immunofluorescence (IF) staining and PCR for detection of P. carinii and the results were compared. Pneumocystis carinii was detected in 4, 8 and 13 sputum samples by cytological staining, IF test and PCR, respectively. Specific amplification bands were obtained in all sputum samples that were positive by both other tests. All tests gave negative results in sputum samples obtained from 5 HIV-infected asymptomatic patients and 22 non-immunosuppressed tuberculosis patients. Our observations suggest that PCR results were well correlated with P. carinii pneumonia (PCP), especially in non-HIV-infected patients. However, PCR positivity obtained in HIV-infected patients could be misleading in the diagnosis of PCP without careful clinical evaluation. Positive results obtained by Giemsa staining or IF test confirm diagnosis of PCP authoritatively. As a result, we suggest testing sputum samples by both PCR and IF techniques for detection of P. carinii.