Gastrointestinal stromal tumors (GISTs), the most common mesenchymal tumors of the intestinal tract, are characterized by the expression of KIT, also known as CD117. Increasingly, primary tumors from novel sites are being described. The KIT gene is commonly mutated, causing constitutive activation of the protein and aberrant growth. Recently, tumors with platelet-derived growth factor receptor (PDGFR)-a mutations have been described in GISTs with wild-type KIT. Factors that predict for an unfavorable outcome are being recognized. A specific molecularly targeted drug, imatinib mesylate, has altered the treatment of this disease. The results of phase I, II, and III clinical trials have consistently demonstrated activity of this agent and elucidated the patient and tumor characteristics associated with response to imatinib. The current challenge in caring for these patients is to identify the appropriate clinical setting for treatment with imatinib and to define the approach to patients whose tumors are insensitive or refractory to imatinib.