Hematopoietic stem cell transplantation (HSCT) is used for treatment of a myriad of both malignant and non-malignant disorders. However, despite many advances over the years which have resulted in improved patient mortality, this subset of patients remains at risk for a variety of post-transplant complications. Pulmonary complications of HSCT are categorized into infectious and non-infectious and occur in up to one-third of patients undergoing HSCT. Infectious etiologies include bacterial, viral and fungal infections, each of which can have significant mortality if not identified and treated early in the course of infection. Advances in the diagnosis and management of infectious complications highlight the importance of non-infectious pulmonary complications related to chemoradiation toxicities, immunosuppressive drugs toxicities, and graft-versus-host disease. This report aims to serve as a guide and clinical update of pulmonary complications following HSCT for the general pulmonologist who may be involved in the care of these patients.