Molecular targeted agents changed the therapeutic pattern on gastrointestinal stromal tumor (GIST). Imatinib  of 400 mg/d is recommended to be the first line therapy for metastatic GIST. Escalation of imatinib dose or sunitinib could improve the overall　survival of patients when the treatment with standard dose of imatinib failed. In addition, new targeted agents　showed potential anti－tumor efficacy. Imatinib adjuvant therapy could improve the recurrence　free survival of GIST patients with median or high risk after complete tumor resection. Preoperative treatment with imatinib raises tumor resection rate, but whether it could provide survival benefit has not been proved. C－kit/PDGFRα gene mutation can predict the efficacy of imatinib and sunitinib, and it is helpful to screen out the GIST patients to receive imatinib adjuvant therapy.