The outcome of patients with gastrointestinal stromal tumors has been dramatically improved by therapy with imatinib mesilate (imatinib mesylate), a KIT and platelet-derived growth factor (PDGFR) tyrosine kinase inhibitor. Unfortunately, the majority of patients eventually experience disease progression due to drug resistance. Recent elucidation of the mechanisms of resistance to imatinib, particularly the acquisition of secondary mutations of the KIT and PDGF receptors, has provided significant insight and potential for the development of novel therapies. This review discusses the efficacy of sunitinib, which is approved for the treatment of patients with imatinib-resistant tumors, and highlights a number of emerging second-generation receptor tyrosine kinase inhibitors that show therapeutic potential in imatinib-resistant patients. Also considered are several promising agents targeting pathways downstream of the constitutionally activated KIT and PDGF receptors. Strategies to overcome imatinib resistance by optimizing combination therapy and selecting specific kinase inhibitors based on the secondary mutations identified in tumors of individual patients are presented.