【Abstract】 Objective To investigate cyclooxygenase (COX) metabolic pathwayrelated gene polymorphisms and their relationship to the incidence of ischemic stroke in southern China. Methods Acute ischemic stroke patients (n=299) were divided into carotid vulnerable plaque group, stable plaque group, none plaque group, a carotid intima thickening group and none intima thickening group, according to the results of carotid Bmode ultrasonography. Genetic polymorphisms of prostaglandin H synthase 1 (PTGS1—rs1236913), prostaglandin H synthase 2 (PTGS2—rs689466), thromboxane A2 synthase (TBXAS1—rs2267679, rs41708, rs194149), prostaglandin E synthase (PTGES—rs6478818), prostacyclin synthase (PTGIS—rs5602, rs5629) were determined using polymerase chain reaction and mass spectrometry analysis. Results The distribution of TBXAS1—rs194149 GG genotype (P=00281), PTGIS—rs5602 CT genotype (P=00319) showed significant differences between the vulnerable plaque and none plaque groups. The distribution of PTGS2—rs689466 GG genotype (P=00216) showed significant differences between the intima thickening and none intima thickening groups. Multivariate logistic regression analysis showed the AA genotype of PTGIS (P=00308, OR: 0275, 95%CI: 00790955) and the AG+GG genotype of PTGS2 (P=00065, OR: 2162, 95%CI: 12323795) were destructive factor for intima thickening. Conclusion The single nucleotide polymorphism (SNP) of COX genes link with the incidence of cerebral infarctions. The further studies show that PTGIS and PTGS2 genes polymorphism related with intima thickening in patients with stroke.