Abstract: We reported one patient with rare malformation, congenital lower vaginal atresia with vesico-vaginal fistula, and introduced the characteristics of this case encompassing clinical symptoms, examinations, diagnosis and management. Meanwhile, we reviewed previously reported similar cases to help clinical physicians better understand urogenital system malformation. When periodic hematuria without vaginal menstrual bleeding occurs in puberty, congenital vaginal atresia with vesico-vaginal fistula should be suspected. Imaging examinations and cystoscopy are important adjuvant diagnostic methods. The only treatment of this disease is surgical incision of the vaginal atresia for drainage and repair of the fistula tract.