We evaluated the incidence, risk factors, and clinical outcome of late-onset non-infectious pulmonary complications (LONIPC) in 599 patients who underwent hematopoietic allogeneic stem cell transplantation (HSCT). The 2-year cumulative incidence of LONIPC was 10% among the 438 patients surviving more than 3 months after HSCT. Transplants from an unrelated donor and occurrence of extensive chronic graft-versus-host disease were the variables significantly associated with the development of LONIPC. The 5-year overall survival was significantly worse among patients with LONIPC than among those without (34% vs 65%, p=0.009). Causes of death were respiratory failure and infections. The relapse rate was similar in the two groups.