Tens of thousands of patients undergo hematopoietic stem cell transplantation (HSCT) each year, mainly for hematologic disorders. In addition to the underlying diseases, the chemotherapy and radiation therapy that HSCT recipients receive can result in damage to multiple organ systems. Pulmonary complications develop in 30% to 60% of HSCT recipients. With the widespread use of prophylaxis for certain infections, the spectrum of pulmonary complications after HSCT has shifted from more infectious to noninfectious complications. This article reviews some of the noninfectious, chronic pulmonary complications.