Gastrointestinal stromal tumors (GISTs) represent the most common mesenchymal neoplasms of the GI tract. The optimal management of GISTs has been evolving rapidly over the past 5 years and depends on proper histopathologic and radiologic diagnosis as well as appropriate multidisciplinary medical and surgical treatments. Complete surgical resection of primary localized GIST with negative margins remains the best therapeutic option today. In the setting of locally advanced or metastatic disease, imatinib mesylate has emerged as the initial treatment of choice, administered either as cytoreductive or as definitive treatment. Surgery or ablative modalities in this setting are becoming increasingly employed, particularly when all disease becomes amenable to gross resection or destruction, or to manage complications arising from the disease following imatinib failure. We report on the surgical management of an unusual and clinically significant complication following progression of disease secondary to imatinib resistance. The role of surgical therapy in the management of GIST complications following resistance to imatinib and the integration of surgical and molecular therapy of locally advanced or metastatic GISTs are discussed.