Lung injury limits the success of allogeneic stem cell transplantation (SCT). The overall incidence varies from 30 to 50% and non-infectious causes occur in one-third to one-half of these. We reviewed pulmonary complications in 369 consecutive patients who received a partially T-cell-depleted myeloablative allogeneic hematopoietic SCT at our institution between 1993 and 2003. All patients were treated uniformly with cyclophosphamide followed by total body irradiation. Control subjects were matched on sex, underlying diagnosis, age, type of transplantation and cytomegalovirus (CMV)-serostatus. Sixty-one patients (16.5%) developed pulmonary complications. Twenty-one patients (5.7%) developed infectious pneumonia. Forty patients developed non-infectious complications which were further subclassified as bronchiolitis obliterans (3.5%), bronchiolitis obliterans-organizing pneumonia (0.5%), diffuse alveolar hemorrhage (0.8%), idiopathic pneumonia syndrome (5.5%) or mixed etiology (0.5%). Acute graft-versus-host disease (GVHD) ⩾grade II was significantly more common in pulmonary patients than in the controls (36/61 versus 22/61 patients, P=0.02). There was no significant difference in the incidence of chronic GVHD ( P=0.09). CMV reactivation was significantly more frequent in patients with lung injury ( P=0.02). Median survival was 41 weeks for the pulmonary patients and 350 weeks for the controls ( P=0.001). Altogether, the incidence of pulmonary complications is low after T-cell-depleted SCT and is associated with acute GVHD and CMV reactivation.