Hematopoietic stem cell transplantation is a recognized treatment for hematological diseases such as leukemia and lymphoma, certain solid organ tumors, and a limited number of immunologic disorders. The major risks associated with this procedure are infections and development of graft-vs-host disease. Bacterial or viral agents are the most common cause of infections, but fungal and protozoan organisms may also be isolated. Bacterial infections occur most frequently in the first 30 days after transplant, whereas the onset of viral infections usually occurs later during the first three months posttransplant. Studies have demonstrated that there are a variety of predisposing factors that influence the type of infection a patient develops. These include underlying disease, type of chemotherapy regimen, type of antimicrobial and antiviral regimen, presence of graft-vs-host disease, and period of severe neutropenia posttransplant. Of these, the period of neutropenia appears to be the most significant. Graft-vs-host disease is seen in those patients who have received allogeneic hematopoietic stem cell transplants. New antimicrobial and antiviral agents and manipulation of the hematopoietic stem cell transplant to select specific cell types for infusion have provided some methods to prevent or decrease the number and severity of infections or to prevent/control graft-vs-host disease.