Introduction: The earliest known human adult stem cells are the so called side population (SP) stem cells which were identified by their unique capacity to rapidly efflux the fluorescent dye Hoechst 33342. From a neuromuscular injury prospective, these stem cells are attractive because they have the proven multi-potent capacity to engraft both muscular and vascular cell types in vivo. However, their current method of isolation is both laborious and mutagenic to cells. The purpose of this study was to develop a rapid non-toxic method of SP stem cell isolation enabling their application to human surgical tissues on the same day of surgery. Methods: By using a candidate receptor approach, we developed a novel peptide antibody called BPS1 which recognizes an extracellular epitope on the ABCG2 half ATP transporter. Human gracilis muscle was Percoll-fractionated and applied to a BPS1 immuno-magnetic purification column. Purified cell populations were then subjected to Hoechst 33342 staining and subjected to FACS analysis. Results: The purified BPS1 cell population displayed a nearly pure SP population profile. BPS1 cells can be isolated from bone marrow and peripheral blood as well. BPS1 cells are distinct from muscle satellite cells, but often co-localize with satellite cells in the interstitial compartment. Furthermore, transplantation of human BPS1 cells into acutely denervated mouse hindlimb muscle retards the rate of muscular atrophy and interstitial fibrosis. Conclusion: In order to fully exploit early adult stem cells in clinical applications, we have developed a novel method for the isolation of SP stem cells using an immuno-magnetic purification procedure. This method has the significant advantages of being non-toxic to stem cells and rapid. Furthermore we will present preliminary animal data supporting a role of BPS1 cells in deterring the muscular atrophy associated with muscle denervation.