The occurrence of a ventral cystic lesion of the penis should alert the clinician to the diagnosis of a median raphe cyst. The lesions, which are most common near the glans penis, may occur anywhere from the urethral meatus to the anus. Cysts of the median raphe represent defects in the embryologic development of the genitalia and are usually lined by entodermal epithelium. Surgical excision is the treatment of choice.