Certain HMB-45-positive epithelioid cell tumors have recently been categorized under a unified concept: perivascular epithelioid cell tumor (PEComa). In this report, we describe ajejunal PEComa arising in a 32-year-old woman without other tumors or stigmata of tuberous sclerosis. The tumor consisted of nests of epithelioid cells with clear to granular eosinophilic cytoplasm. The nests were separated by thin fibrovascular septa. The tumor cells were positive for HMB-45 and progesterone receptor, and negative for cytokeratin, epithelial membrane antigen, vimentin, desmin, alpha-smooth muscle actin and CD34. RT-PCR analysis failed to reveal fusion transcript ETW/ATF1, which is characteristic of clear cell sarcoma of the soft parts. She developed a recurrent tumor at the pelvic wall and the left ovary at 13 and 25 months after the first operation, respectively. Each tumor was resected surgically, and no additional therapy was performed. We think the tumor of this case is a malignant form of PEComa because of the clinical history of multiple recurrences and the size of the primary tumor. Our case underscores that to make a correct diagnosis, clinical information and immunohistochemical examination are essential.