The aim of this in vivo study was to determine the existence of muscle-derived stem cells (MDSCs) in rat corpus cavernosum. Immunohistochemical and RT-PCR analyses were performed to determine the expression of the stem cell markers (Sca-1, Oct4, and desmin) in Sprague-Dawley (SD) rats in different age groups (10 rats in each group). Sca-1 was mainly expressed in blood vessels and cavernous sinus and demonstrated primarily cytoplasmic staining. Desmin was expressed mainly in muscle tissues and staining occurred mainly in the cytoplasm but also partially in the nucleus. An extremely small amount of double-positive stained cells (Sca-1/desmin) were detected near the cavernous sinus. Expression of the markers was significantly and negatively correlated with the age of the rats (P < 0.05). The RT-PCR results showed that the expression levels of Sca-1 and desmin significantly decreased with age (P < 0.05). Correlation analysis indicated that the expression of Sca-1 and desmin were significantly and negatively correlated with the age of rats (r = -0.929, P < 0.05). The present study provides evidence for the existence of MDSCs in rat corpus cavernosum. MDSCs may have therapeutic potential in the treatment of organic erectile dysfunction.