Malignant mesenchymal tumors of the gallbladder are exceedingly rare. We report a malignant stromal tumor of the gallbladder with a phenotype of interstitial cells of Cajal. To our knowledge, only the benign counterpart of this tumor has been described previously. A 34-year-old woman presented with right upper quadrant abdominal pain. At the time of cholecystectomy, the gallbladder was noted to have a thickened wall and a polypoid mass arising in the neck of the gallbladder. Histologic sections showed a cellular proliferation of spindle neoplastic cells that were arranged in short fascicles. Numerous mitotic figures and foci of necrosis were noted. The neoplastic cells expressed CD117 (c-Kit protein) and vimentin. They were negative for smooth muscle actin, desmin, myoglobin, cytokeratin, S100 protein, and CD34. Our case demonstrates that a malignant stromal tumor that is histologically and immunohistochemically identical to gastrointestinal stromal tumor can occur in the gallbladder, and that the expression of CD117 may be of therapeutic importance.