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Ovarian germ cell tumors (GCT) are derived from primordial germ cells of the ovary. Choriocarcinomas are more commonly of placental than ovarian origin in a woman. Vaginal choriocarcinoma is seen very rare in the literature. If the germ cell tumors are relapsed or refractory to the salvage chemotherapy, autologous hematopoietic stem cell transplantation (AHSCT) can be used for the treatment. Our aim is to present a rare vaginal choriocarcinoma patient who underwent AHSCT due to the relapsed disease. A 46-year-old woman who had two vaginal deliveries 18 years ago, presented with a vaginal mass. The diagnosis was made as choriocarcinoma after abscess drainage. Due to the elevated levels of β-HCG, she had undergone chemotherapy. After the four lines chemotherapy serum tumor markers remained high. Because of that reason, AHSCT was performed and after the transplantation, the β-HCG level has decreased. The patient was observed with a very good partial response. According to current literature, AHSCT is a reasonable treatment option for relapsed or resistant cases. In conclusion, our case is the first and unique who has undergone AHSCT. AHSCT is an effective and tolerable treatment for ectopic relapsed and refractory choriocarcinoma cases. [ABSTRACT FROM AUTHOR]