Patients receiving allogeneic marrow transplantation for hematologic malignancies commonly are conditioned with total body irradiation (TBI) and given methotrexate (MTX) in an attempt to prevent graft-versus-host disease. To study the effects of TBI with or without MTX on bronchoalveolar cells and proteins, we performed sequential bronchoalveolar lavages in dogs before and after irradiation. Ten dogs received 9 Gy TBI followed by autologous marrow grafts. Six dogs were given no additional treatment and four also received MTX at 0.4 mg/kg on days 1, 3, 6, and 11- and then weekly until day 100. TBI alone resulted in a significant decrease in alveolar macrophages and lymphocytes with recovery after day 30. The addition of MTX resulted in a more profound and prolonged decrease in alveolar macrophages and lymphocytes. The addition of MTX was also associated with a significant increase in alveolar granulocytes with a concomitant rise in lavage protein content in one animal. Lavage fluid IgA levels remained constant. We conclude that the irradiation and chemotherapy used in marrow transplantation has significant pulmonary effects and may contribute to the pulmonary complications following marrow transplantation.