Hematopoietic stem cell transplantation (HSCT) is an established treatment for a variety of malignant and nonmalignant conditions. Pulmonary complications, infectious and noninfectious, are a major cause of morbidity and mortality in these patients. The recent advances in prophylaxis and treatment of infectious complications increased the significance of noninfectious pulmonary conditions. Acute lung injury due to diffuse alveolar hemorrhage or idiopathic pneumonia syndrome are the main acute complications, while bronchiolitis obliterans remains the most challenging pulmonary complications facing clinicians who are taking care of HSCT recipients. There are other noninfectious pulmonary complications following HSCT that are less frequent. This report provides a clinical update of the incidence, risk factors, pathogenesis, clinical characteristics and management of the main noninfectious pulmonary complications following HSCT.