DNA amplification and silver staining were used to identify Pneumocystis carinii in bronchoscopic lavage and induced sputum samples during 51 episodes of respiratory illness in 47 subjects with HIV infection. In 20 episodes, in which the clinical diagnosis was pneumocystis pneumonia (PCP), silver stain was positive in 14 lavage samples (70%) and 7 sputum samples (35%), whereas DNA amplification was positive in 19 lavage samples (95%) and 18 sputum samples (90%). DNA amplification was positive in only 1 of 31 patients without PCP (PCP developed in this patient within 10 weeks). DNA amplification on induced sputum offers a powerful technique for diagnosis of PCP.