Median raphe cysts of the perineum are uncommon congenital lesions of the male genitalia. They can be found all the way from the distal penis and scrotum toward the perineum in a midline position. They are considered as congenital alterations in embryologic development. A case of a 6 year-old boy is presented. Review of the literature relevant to children was made regarding the embryologic, diagnostic, and treatment aspects. We believe it is important that adult and pediatric urologists recognize these lesions and their management to provide the appropriate information to the parents.