Hematopoietic progenitor/stem cell transplantation (HSC) remains an important treatment strategy for patients with marrow failure syndromes, inherited hematological disorders, and advanced hematological malignancies. Identification of HSCs in mouse and subsequently humans was initially through assays for clonogenic precursors in the form of long-term culture initiating cells and colony-forming units. Graft-versus-host disease (GvHD) is one of the commonest and most challenging complications arising after allogeneic stem cell transplant. Allogeneic donors carry the risk of causing GvHD, and this is strongly linked to human leukocyte antigen (HLA) match. It has been increasingly recognized that immune mechanisms, the graft versus malignancy effect, is an important factor in preventing disease relapse after allogeneic transplant. The most common early complications occur as a consequence of the aplasia due to the conditioning regimen and gastrointestinal toxicity. The major indication for hematopoietic stem cell transplantation is for management of high risk or advanced hematological malignancy.