Between January 1987 and December 1988, 26 immunocompromised children (aged 15 months to 17 years) underwent bronchoalveolar lavage (BAL) for evaluation of pneumonia (chemotherapy for malignancy, 12; orthotopic liver transplantation, 9; other hematologic disease, 5). Bilateral diffuse pulmonary disease was present in 25 children. All were receiving broad spectrum antibiotics. In addition, five were receiving antiviral therapy and two were receiving antifungal therapy. Sixteen patients underwent rigid and 10 underwent flexible bronchoscopy. Two lavages of 10 to 20 mL of normal saline were obtained from involved subsegmental bronchi of both lungs in each patient. Second wash samples from each lung were sent for bacterial and viral cultures, silver staining for pneumocystis, and direct electronmicroscopy analysis for viral particles. Samples were considered satisfactory if they contained an abundance of alveolar macrophages and only small numbers of upper respiratory tract epithelial cells. Alveolar macrophages were present in 21 (81%) of the BAL samples. A specific infectious agent was identified in 15 of these patients (cytomegalovirus [CMV], 6; Pneumocystis carinii, 4; gram-positive cocci, 3; Candida albicans, 2), and therapy was modified in 12. In the five patients in whom BAL samples were contaminated with upper respiratory tract cells no infectious agents were isolated. Because of continued clinical deterioration, open-lung biopsies were performed in three patients in whom BAL had identified CMV and in three patients in whom no organisms had been obtained. Lung biopsies did not identify any new infectious agents, although in the latter group specific histological diagnosis of a noninfectious process was made (hemorrhagic infarct, bronchiolitis obliterans, and lymphoma).(ABSTRACT TRUNCATED AT 250 WORDS)