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Transverse vaginal septum is a rare occurrence. When it co-exists with cervical dysgenesis, it is even rarer. Primary amenorrhea with cyclic pain is one manifesta-tion in post-pubertal women. A case of transverse vaginal septum with vaginal atresia and cervical dys-genesis is presented. Presentation as a huge abdominal mass and severe anaemia posed diagnostic challenges. A two-staged management is described as well as variation in management of the septum. The involve-ment of the patient in her follow up is also stressed.