A median raphe cyst is a dermal cyst resulting from an embryologic irregularity causing a defect in the closure of the median raphe, or an irregular development of ectopic periurethral glands of Littre, or irregular budding and separation of urethral columnar epithelium from the urethra.

A cystic inclusion can occur anywhere along the midline raphe that extends from the urethra to the anus. Usually, the cysts are seen on the ventral aspect of the penis near the glans. The cyst walls usually consist of pseudostratified columnar epithelium, but there have been a few reports of ciliated epithelium. The cyst wall is not attached to the overlying epithelium.