A 5-week-old female infant with vertical HIV-1 exposure, progressive cough, and failure to thrive was given a diagnosis of bilateral diffuse nodular lung lesions. The child was without fever, leukocytosis, anemia, peripheral adenopathy, or hepatosplenomegaly, and the results of repeated blood tests for HIV-1 DNA were negative. A needle biopsy of the lungs revealed granulomatous inflammation and giant cells, with fungal organisms suggestive of Aspergillus species. A nitroblue tetrazolium dye test performed on the patient's blood specimen demonstrated absence of dye reduction, suggesting a diagnosis of chronic granulomatous disease. Further analysis revealed that the child had a deficiency of the p47(phox) component of the nicotinamide adenine dinucleotide phosphate oxidase system. Thus this child with vertical HIV-1 exposure and diffuse pulmonary nodules actually had an autosomal recessive form of chronic granulomatous disease. This case study clearly demonstrates that children with suspected HIV-1 infection might also need evaluation for primary immunodeficiency and that the clinical immunology laboratory is a powerful adjunct in coming to a correct diagnosis.