Six 3-month-old BALB/c Rag2-/- mice developed dyspnea 10 days after intravenous injection of wild type BALB/c CD45RB(high) lymphocytes to induce colitis as a model of inflammatory bowel disease. The lungs of all 6 mice were diffusely gray-purple and did not collapse completely. Microscopic findings were extensive coalescent patchy to diffuse alveolitis, characterized by macrophages and multinucleate giant cells, lymphocytes in alveolar lumina and septa, alveolar luminal of neutrophils, and alveolar proteinic material containing small black vesicular bodies characteristic of Pneumocystis sp. in methenamine silver stained sections. The morphologic diagnosis was diffuse granulomatous pneumonia with intra-alveolar organisms consistent with Pneumocystis sp., with an unusually aggressive inflammatory response related to the experimental procedure and possibly to the BALB/c genetic background.