Spermatogonial stem cells (SSCs) reside in undifferentiated type-A spermatogonia and contribute to continuous spermatogenesis by maintaining the balance between self-renewal and differentiation, thereby meeting the biological demand in the testis. Spermatogonia have to date been characterized principally through their morphology, but we herein report the detailed characterization of undifferentiated spermatogonia in mouse testes based on their gene expression profiles in combination with topological features. The detection of the germ cell-specific proteins Nanos2 and Nanos3 as markers of spermatogonia has enabled the clear dissection of complex populations of these cells as Nanos2 was recently shown to be involved in the maintenance of stem cells. Nanos2 is found to be almost exclusively expressed in A_s to A_pr cells, whereas Nanos3 is detectable in most undifferentiated spermatogonia (A_s to A_al) and differentiating A₁ spermatogonia. In our present study, we find that A_s and A_pr can be basically classified into three categories: (1) GFRα1⁺Nanos2⁺Nanos3⁻Ngn3⁻, (2) GFRα1⁺Nanos2⁺Nanos3⁺Ngn3⁻, and (3) GFRα1⁻Nanos2^±Nanos3⁺Ngn3⁺. We propose that the first of these groups is most likely to include the stem cell population and that Nanos3 may function in transit amplifying cells.