The presence of stem cells in the organ of Corti raises the hope of regeneration of mammalian inner ear cells. However, little is known about the distribution of endogenous stem cells in the inner ear as well as their sphere-forming abilities. The aim of this study is to evaluate the stem cells derived from different turns of the organ of Corti and analyze the sphere-forming capabilities of these stem cells. We dissected and isolated cochleae from postnatal day 1, 7 and 14 mice to separate organ of Corti into apical, middle and basal turns for cell isolation. Our results show that different turns of the organ of Corti harbor distinctly different populations of stem cells. Apical turn-derived cells give rise to more sphere-forming cells than middle and basal turn-derived cells, and middle turn-derived cells give rise to sphere cells number significantly higher than basal turn. Our findings indicate that apical turn of young age murine organ of Corti is best suited for isolation of endogenous stem cells for regeneration of hearing loss.