Aim: To highlight the complications of partial transverse vaginal septum. Background: The transverse vaginal septum is one of the rarest anomalies of the female genital tract with an incidence of 1:70,000 women. Most often the diagnosis of the partial transverse vaginal septum is first made in labor. In an inexperienced hand, the partial transverse vaginal septum can be initially mistaken as a well effaced and partially dilated OS. Case discussion: A 22-year-old unbooked primigravida, presented at 38 weeks in latent labor. On examination, her gestational age corresponded to term, fetus in cephalic position. Fetal heart rate 140–150/minutes. Per vaginal examination raised suspicion of the partial transverse vaginal septum as the finding was a blind pouch with 1 cm aperture and consistency of septum differed from the effaced cervix. Cervix could not be separately felt. Speculum examination revealed a transverse septum at upper one-third of the vagina with a central opening of 1–2 cm. The patient was reevaluated in active labor, and the septum felt thick, she was posted for emergency LSCS to prevent extensive vaginal lacerations or obstructed labor. Postoperative period she was reexamined and it revealed a blind pouch with a central opening, anterior lip of cervix was seen partially through the aperture. Lochia was draining through the opening. Uterus involuted in two weeks. Conclusion: Antenatal assessment of septal thickness by trans vaginal sonography can aid in planning the mode of delivery. Women with thin transverse vaginal septum can safely undergo a trial of labor. Diagnosis of the thick partial transverse vaginal septum is necessary to prevent the patient from having extensive vaginal lacerations or obstructed labor by posting for emergency LSCS.