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Introduction : Transverse vaginal septum is rare outflow tract disorders that may sometimes cause primary amenorrhea. Aims and objectives : To report a case of transverse vaginal septum as a cause of Hematometrocolpos Materials and methods : We report a case of 13 year old with lower abdominal pain since 3 days. She had history of chronic cyclic abdominal pain.On per abdomen uterus is corresponding to 14 weeks size and tenderness is present in hypogastrium. On local examination external genitalia is healthy. Per vaginally hymenal opening is present, vagina admits 1 inch, thick palpable transverse septum present. Results : The patient underwent surgical excision of septum. That consisted of making a transverse incision in the center of vaginal septum draining the hematometrocolpos. Discussion : A vaginal septum is an uncommon outflow tract disorder that occurs due to a fusion defect resulting in a fibrous band of variable thickness within the vaginal canal .TVS are commonly classified on the basis of their location: low (1 4 %), mid (40 %), and high TVS (46%) Conclusion : The transverse vaginal septum remains a rare anomaly of female genital tract. Hematometrocolpos remains a main consequence of this. The management is essentially based Of surgery while taking into account the risks Of postoperative stenosis and repercussions on upper genital tract.