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Mammalian spermatogenesis is a complex but well-coordinated process in which spermatogonial stem cells (SSC) of the testis develop to form spermatozoa. During testicular homeostasis, the spermatogonial stem cells self-renew to maintain the stem cell pool or differentiate to form a progeny of germ cells which sequentially transform to spermatozoa. Accumulating evidence from clinical data and diverse model organisms suggest that the fate of spermatogonial stem cells towards self-renewal or differentiation is governed by intrinsic signals within the cells and by extracellular signals from the SSC niche. Here, we review the past and the most recent developments in understanding the nature of spermatogonial stem cells and the regulation of their homeostasis in mice. We also review the potential clinical applications of spermatogonial stem cells in male infertility as well as in germline modification, by virtue of gene correction and conversion of somatic cells to biologically competent male germline cells.