Bone marrow transplantation is being utilized with increasing frequency in the treatment of patients with malignancy; it is also being applied to the treatment of patients with genetic diseases and as an adjunct to solid organ transplantation. The high dose cytotoxic chemotherapy, often accompanied by total body irradiation, results in severe catabolism, disruption of the gastrointestinal mucosa and marked immunosuppression. A variety of studies show that the supplementation of the amino acid glutamine, by the enteral or parenteral route, as either the free or dipeptide form, appears safe and efficacious in patients undergoing bone marrow transplantation. Further double-blind controlled clinical trials of glutamine supplementation in patients undergoing bone marrow transplantation and receiving more contemporary treatment, which often includes the administration of novel combinations of cytoreductive agents and hematopoietic growth factors, are warranted.