Background: Diagnosing a cause of primary amenorrhea can be challenging when multiple organ systems are affected. This article presents a patient with the rare combination of hypoplastic vagina, partial vaginal septum, and hypogonadotropic hypogonadism where surgical correction, hormone therapy, and vaginal dilation resulted in normal menstruation and sexual function. Case: A 34-year-old woman presented with primary amenorrhea and inability to have coitus. Examination revealed a 1.5-cm vagina ending in a blind pouch. Pelvic ultrasound confirmed the presence of bilateral ovaries, hypoplastic uterus, and cervix. No other renal or skeletal abnormalities were noted on magnetic resonance imaging. Laboratory evaluation was consistent with hypogonadotropic hypogonadism. Results: A combination of surgical excision of a partial vaginal septum, postoperative vaginal dilation, and hormonal therapy resulted in cyclic menstruation and acceptable sexual function. Conclusions: This case illustrates the difficulty of making a diagnosis in a patient with a combination of different causes of primary amenorrhea. Accurate and early diagnosis using appropriate imaging studies and endocrine profile is important to avoid treatment delay. ( J GYNECOL SURG 29:19)