Primary vaginal calculi are uncommon in children. Urethral duplication in females is seen to occur in association with complex congenital malformations. We report the case of perianal persistent urogenital sinus with a hypertrophied clitoris with phallic urethra, scrotum-like pouch, uterus didelphys with obstructed hemivagina, and giant colpolithiasis in 46XX female. A 16-year-old presented with pain abdomen and cyclic passage of blood clots per rectum. She had a tender lump in left iliac region, a phallus like protrusion and a ruggous sac below it. Vaginal opening was absent. Computed tomography showed two uterine horns with a separate cervix and distended non-communicating hemivaginas with a large calcified oval mass in the left hemivagina. On exploration, calculus was extracted from the left hemivagina. The large calculus found in the left hemivagina appears to be the cause of all presenting symptoms. It obstructed the left hemivagina, filling the left uterine horn with menstrual blood causing its gradual enlargement and secondary infection. The early diagnosis and prompt referral of such an anomaly can only be ensured in institutional deliveries. For a significant proportion of newborns in the developing world, the ability to afford or even be referred to institutes which deal with such cases is a luxurious affair. We hope to bridge bridging the knowledge, attitude and practice gap that exists in our health-care system with this report.