Transverse vaginal septum is relatively rare anomaly, occurring in about 1 in 70,000 girls [1]. It is a developmental defect in the embryogenesis of the vagina that leads to incomplete fusions between the mullerian duct component and the urogenital sinus component of the vagina [2]. The patients complain about hydrocolpos, primary amenorrhea and cyclic pelvic pain due to the development of hematocolpos [3]. Tumor markers such as CA19-9 and CA125 are commonly used markers in the diagnosis of pelvic masses. CA19-9, a side branch of the Lewis blood group system, is a sialylated Lewis A antigen that is highly expressed by many adenocarcinomas of the digestive tract. The CA125 is expressed in coelomic epithelia such as mullerian epithelium, peritoneum, pleura and pericardium [4]. In the literature, transverse vaginal septum is not considered as a benign gynecological disorder that causes elevation of CA19-9 and CA125. By presenting this case, we wanted to mention about vaginal anomalies that cause elevation of tumor markers with a literature review.