Neoplasms of the small intestine are very rare. Gastrointestinal stromal tumors (GISTs) are one of the new undifferentiated stromal tumors of the gastrointestinal tract diagnosed by immunohistochemistry. We present a case of a malignant GIST arising from the small intestine and report the radiologic characteristics of the tumor and pathological correlation. CT showed a very large, enhancing mass with extensive central necrosis located on the mesenteric side of the jejunum. A perforation into the jejunal lumen was observed by upper GI series. MRI showed a very large tumor which was hypointense on T2-weighted images. Ultrasound revealed a mixed solid and cystic mass. Grossly, the tumor was solid peripherally with extensive central necrosis. Microscopically, it consisted of spindle and epithelioid cells. Immunohistochemically, the cells stained positive for CD34, which is diagnostic of GIST.