Children with hyper-immunoglobulin M (hyper-IgM) syndrome are at increased risk for Pneumocystis carinii pneumonia (PCP), an opportunistic infection often found in immunodeficient hosts. PCP can present with increasing hypoxia, fever, cough, and respiratory distress. We describe a child with hyper-IgM syndrome in whom bronchoalveolar washings were negative for PCP. However, there was an atypical lung response in which caseating granulomas predominated. The histopathology, resembling that found in tuberculosis, stresses the importance of a high index of clinical suspicion and histologic confirmation for early intervention and treatment. Immunocompromised children with rapidly progressive pulmonary disease may require lung biopsy and stains such as GMS to identify PCP.