Female adnexal tumors of Wolffian origin (FATWOs) are rare tumors that arise in the broad ligament from the remnants of the mesonephric duct. Most FATWOs behave in a benign fashion, and there are only 14 case reports worldwide describing malignant FATWOs. The authors report herein the case of a 69-year-old woman with a malignant FATWO, positive for CD56. The mass was composed mainly of solid neoplastic epithelial cells, closely packed, branching, and anastomosing in slender tubules. There was an eosinophilic secretion within the lumens of some of the cysts and tubules. The number of mitoses was somewhat high in the active areas, numberingfive to seven per ten high-power fields. The tumor cells were strongly positive for glutathione S-transferase π, and positive for calretinin, vimentin, c-Kit, CD99, and CD56; neuron-specific enolase was also partially expressed. The tumor cells were negative for inhibin α, estrogen receptors, progesterone receptors, B-cell lymphoma 2, and S100. Taken together, these immunohistochemical and pathological findings gave the diagnosis of malignant FATWO. The patient experienced a recurrence one year after her initial surgery. CD56 immunostaining was negative in two benign FATWO cases at the present institution. These findings suggest that CD56-positivity may be a diagnostic biomarker to differentiate malignant FATWOs from benign lesions.