Spermatogonial stem cells (SSCs) are the basis of male spermatogenesis and fertility. SSCs are distinguished by their ability to self-renew and differentiate into spermatozoa throughout the male reproductive life and pass genetic information to the next generation. Immunohistochemistry (IHC), immunocytochemistry (ICC) and Fluidigm reverse transcriptase-polymerase chain reaction (RT-PCR) were used to analyze the expression of PLZF and VASA in mice testis tissue. In this experimental study, whereas undifferentiated spermatogonial cells sharply expressed PLZF, other types of germ cells located in the seminiferous tubule were negative for this marker. Conversely, the germ cells near the basal membrane of the seminiferous tubule showed VASA expression, whereas the undifferentiated germ cells located on the basal membrane were negative. The ICC analysis indicated higher expression of PLZF in the isolated undifferentiated cells compared with differentiated germ cells. Fluidigm real-time RT-PCR results demonstrated a significant expression (P < 0.05) of VASA in the SSCs compared with differentiated cells and also showed expression of PLZF in undifferentiated spermatogonia. These results clearly proved the role of PLZF as a specific marker for SSCs, and can be beneficial for advanced research on in vitro differentiation of SSCs to functional sperms.