Rhabdoid features in gastrointestinal stromal tumors (GISTs) are rare. To the authors' knowledge, only 51 cases have been reported. Most of these reports consist of case series in which the rhabdoid GISTs comprise a small proportion of the tumors studied. Information regarding site of origin and clinical behavior is sparse. Although the stomach is the only site of origin documented, most reports do not include this data. Malignancy has not been reported, though follow-up is inadequate in most cases to comment on tumor behavior. Exon 11 mutations comprise all previously described KIT mutations, the majority of which are deletions. The authors present the case of a malignant small-intestinal rhabdoid GIST that recurred twice following resection and treatment with tyrosine kinase inhibitors. The tumor harbored a KIT exon 11, 579-580 LY insertion that, to the authors' knowledge, has not been previously reported. This case is the first rhabdoid GIST described in the small intestine and is the first to show documented evidence of malignancy.