Malignant extrarenal rhabdoid tumors had been described in a variety of anatomic locations including gastrointestinal tract. Carcinomas of small intestine are quite uncommon neoplasms, and those with rhabdoid differentiation are exceedingly rare. These poorly differentiated tumors pose a great deal of difficulty in diagnosis as well as in deciding whether they are primary or metastatic in origin because malignant rhabdoid tumors or carcinomas with rhabdoid differentiation of other sites can metastasize to the small intestine. They behave more aggressively than the typical adenocarcinomas of the same location. Herein, we report a 52-year-old patient with primary small bowel malignant rhabdoid tumor, who was completely disease-free after the initial presentation and management. Five years later, he was found to have a lung mass proved to be adenocarcinoma, exhibiting focal giant cell differentiation without rhabdoid features.