A nested polymerase chain reaction (PCR) assay was investigated for detection of Pneumocystis carinii in 96 respiratory tract specimens from 82 children, of whom 28 were immunocompetent but with chronic lung disorders (CLD), eight had AIDS and P. carinii pneumonia (PCP), 16 had AIDS but no respiratory symptoms, and 30 were healthy immunocompetent children. Gomori methenamine silver stain (GMS) and indirect immunofluorescence assay (IFA) were performed in parallel. Of 36 specimens from children with CLD, 12 were P. carinii PCR-positive compared to 10 positive by GMS-IFA. Of eight specimens from children with AIDS and PCP, seven were P. carinii-positive by PCR and six by GMS-IFA, and of 22 specimens from HIV-positive children without respiratory symptoms, two were positive by PCR and none by GMS-IFA. P. carinii DNA was also detected by PCR in blood samples from four children with P. carinii-positive nasopharyngeal aspirates. Specimens from healthy children were negative for P. carinii by both PCR and GMS-IFA. Of the seven children with CLD, who were P. carinii-positive, two had clinical and microbiological improvement with co-trimoxazole treatment, two improved initially but relapsed, and one had P. carinii cysts persistently in follow-up specimens despite co-trimoxazole treatment. These results suggest an association between P. carinii and exacerbations of CLD in childhood, in the absence of HIV infection or other immunodeficiency syndromes.