We herein report the case of a 68-year-old man with a history of allogeneic hematopoietic stem cell transplantation for acute myelocytic leukemia in whom graft-versus-host disease (GVHD) developed in the gastrointestinal tract and liver five months after transplantation. In that same period, chest computed tomography showed infiltration in both upper lungs. We performed bronchoscopy to clarify the GVHD and pulmonary infection. Nocardia nova was identified in the bronchoalveolar lavage fluid, and we diagnosed the patient as having pulmonary nocardiosis. Because the differential diagnosis is important for the medical management of GVHD and pulmonary infection, performing bronchoscopy is essential for making an appropriate and rapid diagnosis.