Imatinib mesylate (STI571) is an oral 2-phenylaminopyrimidine derivative that acts as a selective inhibitor against several receptor tyrosine kinases and has been viewed as one of the therapeutic success stories of the 21st century. Imatinib was first shown to inhibit the causative molecular translocation in chronic myelogenous leukemia, BCR-ABL. Because imatinib could also inhibit the activity of KIT, a 145-kD transmembrane glycoprotein, and because gastrointestinal stromal tumors (GISTs), the most common mesenchymal tumors of the digestive tract, are characterized by expression of a gain-of-function mutation in KIT, imatinib was used in therapeutic trials of GISTs beginning in 1999. The initial success has now resulted in more widespread use of imatinib for the treatment of patients with GIST. Molecular genetic studies have shown that most GISTs possess a KIT mutation in exon 9, 11, 13, or 17. Clinically, GIST patients with KIT exon 11 mutations (ie, the juxtamembrane region) are the most prevalent and sensitive to imatinib. In addition to the inhibitory effect on KIT, imatinib also inhibits the activity of mutant platelet-derived growth factor receptor-alpha (PDGFRalpha) found in a subset of GIST. What is becoming evident is that there are patients with GIST who lack mutations in KIT or PDGFRalpha, or possess "imatinib-resistant" mutations (such as exon 17 mutations in KIT and exon 18 mutations in PDGFRalpha). These patients typically do not respond well to imatinib therapy. Therefore, identifying additional genetic factors that contribute to the pathogenesis of GIST, independent of KIT and PDGFRalpha, will be important in developing additional anti-GIST therapies. As one might suspect from previous experiences with antitumor therapies, primary and secondary resistance to imatinib is also becoming a major clinical problem in the treatment of this disease. Therefore, new drugs that can serve as alternative therapies in imatinib-resistant patients with GIST or that can be used in combination with imatinib will be needed. As with most recent efforts to derive novel molecular target therapies to treat cancer, improved therapy of GIST will continue to benefit from advances in the molecular characterization of this disease.