The transplantation of peripheral blood stem cells and bone marrow (BMT) has been increasing at an enormous pace as the procedure becomes the standard of care for many diseases. Pulmonary complications are common and the most fatal of specific organ failures. Complications are diverse, but the time frame of presentation can narrow the differential diagnosis considerably. Pulmonary edema can be hydrostatic, owing to volume overload or cardiac dysfunction, or nonhydrostatic, owing to capillary leak from cytokine release. Bacterial pneumonia is most common in the first month after transplant. Fungal pneumonia can occur early, as a result of neutropenia, or later, as a result of immunosuppressive therapy. The most common invasive respiratory fungal infection in the BMT population is aspergillosis. Treatment usually requires high doses of amphotericin B and possibly surgery to resect residual disease. Cytomegalovirus (CMV) is the most common cause of interstitial pneumonia after BMT, especially in patients who are seropositive for CMV before transplantation. Other respiratory viral infections have also been reported after BMT. Most pneumonias in the first month after transplant do not have a documented infection and are termed idiopathic pneumonia syndrome. The cause may be related to the conditioning regimen or occult viral infection. Mortality is roughly 80|X%, and the use of steroids for treatment is controversial. Severe airways obstruction, including bronchiolitis obliterans, is a late complication of BMT and is related to chronic graft-versus-host disease. The outcome of patients with respiratory failure who require mechanical ventilation is dismal, but survival has been improving over the last decade. Pulmonary function tests have been used to stratify risk for respiratory complications with varying success, and none are strong enough predictors to absolutely exclude a patient from BMT.