Mammalian spermatogenesis is an intricate process resulting in the formation of male haploid gametes. In order to attain a better understanding of the complexity of this process, the development of a reproducible cytometry method to isolate germ cells is much needed. Here, we describe a reproducible cytometry protocol to isolate germ cells from adult mouse testis. We paid special attention to the optimization of what are considered the most critical steps, including testis disaggregation, antibody titration, cell staining, and germ cell discrimination by FACS.