Atherosclerosis plays an important role in ischemic stroke, and oxidative stress participates in the entire process of atherosclerosis. Glutathione S-transferase (GST) acting with other antioxidant enzymes can eliminate reactive oxygen species and protect cells against oxidative damage. To assess the association of glutathione S-transferase (GSTT1 and GSTM1) gene polymorphisms with ischemic stroke in the Chinese Han population, the present study selected 315 patients with ischemic stroke and 210 healthy controls for comparison. GSTT1 and GSTM1 genotypes were determined using polymerase chain reactions, electrophoresis and imaging analysis. No obvious evidence of GSTT1-null, GSTM1-null and GSTT1/GSTM1-double null genotype distribution differences was found between case and control groups or between genders. Subgroup analysis showed that the risk of stroke was increased when hypertension was accompanied by GSTT1-null (odds ratio (OR) = 2.996, P < 0.001) and GSTM1-null (OR = 3.680, P < 0.001) genotypes; diabetes mellitus was accompanied by GSTT1-null (OR = 1.860, P = 0.031) and GSTM1-null (OR = 2.444, P = 0.002) genotypes, and smokers showed a GSTT1-null genotype (OR = 2.276, P = 0.003). GSTT1- and GSTM1-null genotypes may interact synergistically with hypertension, diabetes mellitus and smoking to increase the incidence risk of ischemic stroke.