We report 2 recent cases of midline cysts of the genitoperineal raphe in children, and discuss the embryogenesis, diagnosis and management. Congenital anomalies of an unclear etiology, median raphe cysts are probably more common than has been reported in the literature. Medical attention is usually sought for secondary infections or pain with intercourse. Awareness and prompt identification of these entities by urologists are essential for proper management when differentiation from other more formidable lesions, including urethral diverticula, becomes important. Simple surgical excision is effective in most cases.