We report a patient with myelodysplastic syndrome who underwent an allogeneic bone marrow transplantation during the first remission. On day 110 he had a low-grade fever and pulmonary nodules, without superficial lymphadenopathy, were observed. The pulmonary nodules gradually increased in size and in number despite administration of anti-fungal and anti-tuberculosis agents. Transbronchial lung biopsy was performed on day 204, yielding a diagnosis of polyclonal post-transplant lymphoproliferative disease (PTLD) positive for Epstein-Barr virus (EBV)-encoded RNA (EBER) and CD20. Subsequent measurement of herpesvirus viral load demonstrated a consistent elevation of EBV viral load from day 96 to day 221. After treatment with anti-CD20 monoclonal antibody (rituximab), regression of pulmonary nodules was confirmed and the number of EBV genome copies decreased to a normal range. This case suggests that monitoring the quantitative EBV viral load may be necessary in cases of EBV-associated PTLD, even in cases presenting pulmonary nodules. Solitary pulmonary nodules may be a rare symptom of PTLD, but in such cases, an aggressive approach may be necessary to obtain a correct diagnosis.