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Stem cells in various somatic tissues (bone marrow, skeletal muscle) can be identified by the `Side Population' marker based on Hoechst 33342 efflux. We show that mouse testicular cells also display a `Side Population' that express Bcrp1 mRNA, the ABC transporter responsible for Hoechst efflux in hematopoietic cells. Inhibition of Hoechst efflux by specific BCRP1 inhibitor Ko143 show that germinal `Side Population' phenotype is dependent on BCRP1 activity. Analysis of two well-defined models of altered spermatogenesis(W/W<sup>v</sup> mutants and cryptorchid male mice) and RNA expression studies of differentiation markers demonstrate that germinal `Side Population' contains spermatogonial cells. In addition,α ₆-integrin and Stra8 germinal stem cell markers, are expressed in the `Side Population'. In vivo repopulation assay clearly establishes that testis `Side Population' in adult mice is highly enriched in male germ …