Although median raphe cysts of the penis have been widely reported the pathogenesis is obscure. We describe the microstructural detection of 3 cases of median raphe to study the true pathogenesis. Three patients presented to our clinic of plastic surgery complaining of abnormal shape of the penis or mass recurrence. High magnification light microscopy and electron microscopy were performed. Microstructural study revealed that all 3 cases had similar findings to those of the common urethral mucosa. Median raphe cysts are derived from the external paraurethral ducts and contain features that to our knowledge have not been previously reported.