As more individuals survive their hematologic malignancies after allogeneic hematopoietic stem cell transplantation (HSCT), there is growing appreciation of the late organ complications of this curative procedure for malignant and nonmalignant hematologic disorders. Late noninfectious pulmonary complications encompass all aspects of the bronchopulmonary anatomy. There have been recent advances in the diagnostic recognition and management of bronchiolitis obliterans syndrome, which is recognized as a pulmonary manifestation of chronic graft-versus-host disease. Organizing pneumonia and other interstitial lung diseases are increasingly recognized. This article provides an update on these entities as well as pleural and pulmonary vascular disease after allogeneic HSCT.