Hematopoietic stem cell transplantation(HSCT) increase the chances of cure of many hematological malignancy. The clinical laboratory plays a major role in support of HSCT. Both transplantation-specific laboratory test(tissue typing, assessment of graft viability/rejection, evaluation of minimal residual disease, and measurement of immunosuppressive drugs) and routine clinical laboratory tests(biochemical, hematological, serological, urinary, bacteriological, and physiological examinations) are significant. Hematopoietic stem cells(HSC) are usually assessed as CD34+ cells, while immature cells determined by automated hematology analyzers can simply evaluate HCS. These automated immature cell counts are earlier markers of engraftment following transplantation than the traditional indicators(neutrophils and platelets). After transplantation, infections, regimen-related toxicities, graft-versus host disease, veno-occlusive disease, and thrombotic microangiopathy are the serious complications, which are causes of expected mortality and morbidity in HSCT. Clinical laboratory monitoring may contribute early diagnosis and treatment of the complications, resulting in prevention of the adverse events.