We evaluated the clinical value of polymerase chain reaction (PCR) for screening Pneumocystis carinii pneumonia (PCP) in non-HIV-infected immunocompromised patients. We retrospectively analyzed PCR and Grocott's methenamine silver (GMS) staining on 1044 clinical specimens obtained from 756 patients. Positive rates of PCR and GMS staining in sputum specimens were 21.1% and 9.5%, respectively (P < 0.01), and in bronchoalveolar lavage (BAL), specimens were 31.9% and 25.5%, respectively. Among 5 patient groups, the highest GMS staining and PCR positive rates were observed in immunosuppressed patients. In 28 GMS staining-positive patients, positive rates of PCR and GMS staining after a short anti-PCP treatment were 39.3% and 17.9%, respectively. In 5 patients with positive PCR but negative GMS staining results in initial sputum examination, GMS staining result turned positive in Subsequent BAL specimens. In conclusion, PCR is sensitive for detection of Pneumocystis in sputum specimens and is useful for screening PCP in non-HIV-infected high-risk patients. (C) 2009 Elsevier Inc. All rights reserved.