Hematopoietic stem cells (HSCs), isolated from the blood or bone marrow, have the potential to renew itself and can differentiate into various specialized cells. These unique features have made HSCs a promising source of stem cell–based therapy for many diseases, including leukemia, cancer, autoimmune rheumatic diseases, and intestinal diseases. One of the targeted intestinal diseases is Crohn's disease, which is to be treated with autologous stem cell transplantation. However, the most important limiting factor is the inadequate search for a suitable human leukocyte antigen donor for transplantation. This chapter discusses the clinical application of HSCs in various diseases, including intestinal failure.