Objective To determine the effects of cyclooxygenase 2 (COX2) on risk stratification and prognosis of patients with gastrointestinal stromal tumor (GIST). Methods　 Literatures in the Cochrane libraries of clinical comparative trials, PubMed, EMBASE, Cancer Lit and Chinese BioMedical Literature from 1966 to 2012 were retrieved using the Cochrane systematic evaluation method. The original data were extracted and cross checked by 2 reviewers. The indicator for assessment including positive rates of COX 2 in GIST patients withdifferent tumor diameters (<5 cm versus ≥5 cm), mitosis of cancer cells (<5/50 HPF versus ≥5/50 HPF) and National Institute of Health (NIH) risk stratifications (very low+low versus intermediate+high). The relationship between COX2 expression and recurrence and metastasis of GIST was evaluated. All the data were analyzed using the RevMan 5.1 software with Meta analysis. The heterogeneity between studies was analyzed using the I₂. The binary data were presented by odds ration(OR) and 95% confidence interval (95%CI). Results Seven articles with a total of 415 patients were included in the analysis. The COX2 expression did not correlate with the tumor diameters, NIH risk stratifications and tumor metastasis and recurrence (OR=0.60,0.72,2.46,P>0.05), but with the mitosis of cancer cells (OR=0.46,P<0.05). Conclusion COX2 expression is partly correlated with risk stratification of GIST, but has no effect on the prognosis.