Noninfectious conditions are now the major pulmonary causes of morbidity and mortality after hematopoietic stem cell transplantation (HSCT). The idiopathic pneumonia syndrome (IPS) remains one of the more common and serious pulmonary complications within months after transplantation. Epidemiological data suggest that, although graft versus host disease (GVHD) reactions may play an etiological role, the major contributing factor is conditioning-related toxicity. Among lung conditions that are more closely associated with GVHD are both obliterative bronchiolitis (usually occurring months to years after HSCT) and bronchiolitis obliterans organizing pneumonia (BOOP). The former is an inexorably progressive condition, whereas BOOP behaves similarly to idiopathic BOOP seen in other populations. Also addressed in this article are engraftment syndrome, diffuse alveolar hemorrhage, and pulmonary veno-occlusive disease. Knowledge of these complications is now a part of the contemporary practice of pulmonary medicine, no longer isolated to the transplant pulmonologist.