Recent advances in molecular analysis by polymerase chain reaction(PCR) have taken a prominent position an essential part in regeneration medicine. In hematopoietic stem cell transplantation, HLA(human leukocyte antigen) typing, assessment of graft viability/rejection (chimerism analysis), and evaluation of minimal residual disease are significant for treatment strategy. Molecular analysis will play a more important role in the diversification of transplantation methods in the future of tailor-made medicines.