PEComa of the gastrointestinal tract, composed of perivascular epithelioid cells with myomelanocytic differentiation, is rare with previous literature limited to 16 case reports. There is a marked female preponderance and approximately one-third of the cases occur in the pediatric age group. We report PEComa with lymph node involvement occurring in the rectum of a 15-year-old girl, treated by surgical resection and adjuvant chemotherapy. The patient is well at 9 months follow-up with neither radiologic nor endoscopic evidence of recurrence. We review the differential diagnosis of intestinal PEComa, which includes malignant melanoma, epithelioid gastrointestinal stromal tumors, clear cell sarcoma of soft parts, alveolar soft part sarcoma, leiomyosarcoma with HMB45 expression, and paraganglioma. Immunohistochemistry can rule out many of these morphologically similar tumors but differentiation from clear cell sarcoma may require reverse transcription-polymerase chain reaction. We discuss the determination of pathologic features indicative of malignancy in PEComa, which is complicated in the gastrointestinal tract due to the small number of cases, variability of pathologic features reported, and inconsistent reporting of outcome. All 4 tumors reporting early recurrence or progression were greater than 5 cm in size and had areas of coagulative tumor necrosis. In addition, high nuclear grade and lymphovascular invasion were seen in 2 of these 4 cases. We propose that a minimum dataset for gastrointestinal PEComa should include these features along with mitotic count, infiltrative border, and tumor stage analogous to that used in colorectal carcinoma.