Transvaginal septum is a congenital defective disorder. The transverse vaginal septum is caused by the evolution of the vaginal plate during embryonic growth of the urogenital sinus, the vaginal bulb, towards the cephalic end, which is obstructed during luminalization from the bottom up and does not pass through or is not fully luminalized. It often occurs at the junction of the upper and middle third of the vagina, but also occurs anywhere in the vagina up to the tip of the vagina, near the cervix. Complete transverse septum is rare and may result in vaginal atresia; it usually has a small hole in the center or lateral aspect of the septum, which varies in size. In the absence of a hole, the transverse septum may present with periodic lower abdominal pain without menstrual flow. Some patients may have no clinical symptoms. The first thing to look for is the location of the transverse septum, which is rare if it is low, and the second thing to look for small holes in the transverse septum (often in the central part). If there is a hole, a uterine probe can be inserted into the hole to investigate the width and depth of the vaginal cavity above the hole; if there is no hole, a coarse needle can be used to puncture the hole, paying attention to the depth of penetration when drawing out the accumulated blood to estimate the thickness of the septum, and then a surgical probe can be inserted by the puncture hole to understand the width and depth of the vaginal cavity above the septum for a clear diagnosis. Transverse vaginal septum should be differentiated from hymenal atresia. It is not difficult to differentiate based on symptoms and gynecologic examination. However, in case of complete atresia, the symptoms are basically the same as those of hymenal atresia.