Abstract: Objective To investigate the prognostic factors of gastrointestinal stromal tumor(GIST). Methods Clinical data of 349 cases of GIST patients in our hospital between January 2006 and September 2011 were analyzed retrospectively and the prognostic factors were evaluated. Results 335 patients underwent R0 resection and 14 with palliative resection. With a follow-up of 288 (82.5%) patients (median:33 months, range 3-72 months), 61 patients with progressed were observed and 33 of them died. Unconditional logistic regression analysis showed that tumor location (P=0.003, OR=1.412, 95%CI:1.125-1.772), risk classification (P=0.011, OR=2.930, 95%CI:1.278-6.716) and use of imatinib treatment (P=0.009, OR=0.291, 95%CI:0.115-0.734) were independent factors for post-operative recurrence or metastasis. Survival analysis of 128 patients between January 2006 and December 2008, Cox regression analysis demonstrated diameter (P=0.034, OR=2.328, 95%CI:1.065-5.089), risk classification (P=0.015, OR=3.031, 95%CI:1.236-7.428) and use of imatinib treatment (P=0.011, OR=0.259, 95%CI:0.091-0.734) were independent prognosis factors. Conclusions No specific clinical manifestation was observed for GIST. Tumor location, diameter, risk classification and imatinib treatment could influence on prognosis. Radical resection combined with imatinib treatment could improve the prognosis.