Malignant rhabdoid tumor, first described in the kidney of young infants, is a rare and highly aggressive neoplasm of controversial histogenesis that has been reported at many other sites, including the gastrointestinal tract. However, malignant rhabdoid tumor of the small intestine is very rare, with only seven cases published to date. We report a 70-year-old man who presented with abdominal pain and weight loss, and showed a perforated jejunal mass with disseminated metastases by imaging. The patient underwent partial jejunectomy and biopsy of a liver metastasis. Microscopically, the tumor was characterized by neoplastic cells with vesicular nuclei, large nucleoli and abundant eccentric cytoplasm with hyaline globular intracytoplasmic inclusions. Immunohistochemically, the neoplasm coexpressed vimentin and epithelial antigens (AE1/AE3, Cam 5.2, CK34betaE12, CK19 and EMA), most of them showing a peculiar immunostaining pattern in relation to the globular inclusions. Ultrastructurally, the inclusions corresponded to paranuclear whorls of intermediate filaments. The patient received postoperative chemotherapy but died 9 months after surgery. In summary, we report the exceptional case of an undifferentiated carcinoma of the jejunum with rhabdoid phenotype. As with tumors at other sites, recognition of rhabdoid morphology in small intestine neoplasms is of significance because the prognosis is extremely poor.