OBJECTIVE To evaluate the diagnostic value of PCR for detection of Pneumocystis carinii DNA from induced sputum samples. METHODS P. carinii cysts or trophozoites were detected in induced sputa by Giemsa stain or Gomori Methenamine silver (GMS) stain. A fragment of the Pneumocystis carinii mitochondrial large-subunit rRNA gene was amplified from sputum samples using a one-step PCR method with mt-rRNA primers. RESULTS In this study, sputum samples from 16 patients with a clinical diagnosis of Pneumocystis carinii pneumonia (PCP) and 20 patients with other respiratory infections were first tested by cytochemical staining. Pneumocystis carinii was detected in 8 and 0 sputum samples from the two groups, respectively. The sensitivity and specificity of cytochemical stain were 50% and 100%. With the one-step mt-rRNA-PCR method, Pneumocystis carinii DNA was detected in 14 and 0 sputum samples from 16 PCP patients and 20 non-PCP patients. The sensitivity and specificity of mt-rRNA-PCR was 88% and 100%, respectively. CONCLUSIONS The specificity of both Giemsa and GMS staining of induced sputum samples is high and the methods are simple, but the sensitivity is low. The sensitivity of PCR for P. carinii DNA from induced sputum samples is significantly higher than cytochemical stains, and the method is highly specific when used in the clinical diagnosis of PCP.