Embryonic stem cells have the ability to become any cell in the body. Basic studies looking at novel methods of brain repair have reported that stem cell transplantation can restore function and produce new neurons. A critical component of this research is determining what method of detection should be employed to distinguish transplanted cells from the host cells. There are many methods for cell detection ranging from genetically engineering reporter molecule expression to electron microscopy. However, published reports tend to not utilize more than one detection method. The status quo of using one or two levels of cell detection may not be sufficient to support claims of cell identity. For example: In histochemical staining, the contribution of the endogenous mammalian β-galactosidase has to be distinguished from a reporter enzyme. The recent demonstrations of stem cell fusion could greatly impact the interpretation of cell fate following transplantation. There are also immunological results using common techniques that must be interpreted carefully due to the presence of endogenous biotin. We suggest that multiple methods of histological detection must be invoked to increase the confidence of our interpretations of experimental results. These issues need to be fully addressed to realize the full potential of stem cell transplantation.