Pluripotent stem cells have shown great therapeutic promise because of their natural capacity to regenerate damaged tissue. Likewise, autologous stem cells or genetically modified stem cells have already been successfully applied in animal or clinical experimental studies including cardiopathy, diabetic disease, system lupus erythema, pancreatic disease, and liver disease. In these studies regarding stem cell transplants in different diseases, identifying the location of implanted cells and distinguishing them from endogenous cells is the first and most important step. Moreover, different tracing techniques were applied in different studies for their different sensitivity, dynamic range, convenience and reliability of their assays. Therefore, we will here review different tracing techniques and their applications in stem cell transplants, including both experiment studies and preclinical trials.