Chronic granulomatous disease (CGD) of childhood is a rare inherited disease in which phagocytic cells fail to produce the normal respiratory burst in response to infectious stimuli, leaving the patient particularly susceptible to infections with bacteria and fungi that produce catalase. Between 1988 and 1993 at the NIH, 58 pulmonary cytology specimens were obtained on 24 CGD patients. The number of specimens per patient ranged from one to 13 with an average 2.4. The 58 specimens included: 33 bronchoalveolar lavages; one bronchial brushing; 20 lung or pleural mass fine-needle aspirates; three pleural fluids, and one sputum. Two lung aspirates with insufficient material, five bronchoalveolar lavages performed post-treatment to confirm clinical resolution of disease, and two bronchoalveolar lavages not submitted for culture were excluded from further analysis. Of the 49 remaining specimens obtained from patients clinically suspected of having a pulmonary infection, cytology demonstrated a pathogenic organism in nine (18%). Microbiologic cultures were positive in 19/49 (39%). Cytology identified fungus in 8/13 (62%) of documented fungal infections, including four cases where microbiology was negative. Bacterial and mixed bacterial/fungal infections were usually not detected by cytology even with appropriate strains. No organisms were identified by cytology in the four cases of nocardia or the three cases of pseudomonas infection. The combination of cytology and microbiology provided the greatest diagnostic sensitivity, yielding a diagnosis in 22/49 cases (45%). Of the 27 cases with negative cytology and microbiology, an infectious agent was identified in eight upon submission of additional material: three cytology specimens and five tissue specimens. In the remaining 19 cases, no organisms were identified, however, the patients were treated presumptively. Characteristic pathologic features of granulomatous inflammation, necrosis, and giant cells were present in fine-needle aspirates, often when on organisms could be identified, but were not seen in other types of respiratory specimens.