Two major pulmonary diseases were defined on the basis of lung biopsies in 15 children with acquired immune deficiency syndrome (AIDS) or AIDS-related complex. Pneumocystis carinii pneumonia was observed in eight children, and pulmonary lymphoid hyperplasia in six. One child had nonspecific interstitial pneumonitis. Children with P. carinii pneumonia had more severe hypoxemia, with higher alveolar-arterial oxygen gradients, and higher isomorphic elevations of serum lactate dehydrogenase. Clinically, children with pulmonary lymphoid hyperplasia were older, and had digital clubbing, parotid gland enlargement, and elevated serum IgG levels. Results of serologic assays and lung tissue analysis were suggestive of persistent Epstein-Barr virus infection exclusively in patients with pulmonary lymphoid hyperplasia. Recognition of the clinical and laboratory findings characteristic of each entity may assist in the differential diagnosis without the need of surgical biopsy.