Gastrointestinal stromal tumors (GIST) are mesenchymal tumors that occur predominantly in the stomach and the small bowel. Their pathogenesis is generally based on primary activating mutations in the KIT or PDGFRα genes that result in constitutive activation of receptor tyrosine kinase activity. Imatinib, first designed to competitively inhibit the ATP-binding pocket of the BCR-ABL tyrosin kinase exhibits inhibition also in the KIT and PDGFRα tyrosine kinases, which revolutionized the therapy of gastrointestinal stromal tumors, a disease without any systemic treatment options prior to imatinib. Clinical benefit is achieved in approximately 85% of patients with unresectable or metastatic disease with a median progression-free survival of 19 to 26 months and an overall survival approaching 5 years. Disease progression results from different mechanisms of resistance most frequently involving the emergence of secondary mutations in KIT exons 13, 14, or 17. Several newer drugs have been studied in patients failing or being intolerant to imatinib, including the multitargeted agent sunitinib as well as other KIT targeting tyrosine kinase inhibitors like nilotinib or agents targeting alternative pathways like anti-angiogenic agents, mTOR-, RAF kinase- and chaperone inhibitors.