Pure primary ovarian choriocarcinoma is a rare condition that can be of gestational or non-gestational origin. Non-gestational choriocarcinoma has been found to be resistant to single-agent chemotherapy and has a worse prognosis than gestational choriocarcinoma, but it is difficult to distinguish the two types by routine histological examination. Herein is reported a case of primary pure non-gestational choriocarcinoma of the ovary in a 33-year-old nulligravid woman, as confirmed by DNA polymorphism analysis. All tested microsatellite markers had identical DNA profiles with the same allelic sizes between the tumor and the myometrium of the patient, who was homozygous for three markers (BAT26, BAT25 and D17S250) and heterozygous for four (D2S123, D18S57, DCC and D18S58), supporting non-gestational origin. The patient has no evidence of disease 17 months after surgery and four cycles of combination chemotherapy. This case demonstrates the usefulness of DNA polymorphism analysis for the determination of the origin of extrauterine choriocarcinoma. Clinical relevance of this method needs to be further studied and substantiated.