Bronchiolitis obliterans syndrome (BOS) is a progressive, insidious, and often fatal lung allo-reaction that can occur following allogeneic hematopoietic stem cell transplantation (HCT) or allogeneic lung transplantation. Current estimates in the literature suggest that approximately 2% to 3% of all allogeneic HCT recipients and 6% of patients who develop chronic graft-versus-host disease (cGVHD) will develop this syndrome. However, based on newer data it is likely that the true incidence of BOS is higher. Unfortunately, the survival and treatment of patients with BOS after HCT has not improved over the last 20 years. Attempts at clinical trials have been hindered by the lack of uniform diagnostic criteria and inability to detect the syndrome at a reversible stage in its natural history. Recently, the National Institutes of Health (NIH) consensus project for criteria in cGVHD has made recommendations regarding the diagnosis of BOS and monitoring of lung disease among long-term survivors. Although a rare and poorly understood manifestation of cGVHD, BOS occurs commonly after lung transplantation and is similar in pathology, clinical presentation, radiographic presentation, and presumed immunologic pathogenesis. This review describes the current understanding of the epidemiology and pathogenesis of BOS and presents information on evaluations and therapies for patients with BOS after HCT.