Aim To investigate the relationship between plasma homocysteine(Hcy),methylenetetrahydrofolate reductase(MTHFR) gene polymorphisms and carotid artery plaques in the cerebral infarction patients.Methods 128 carotid system cerebral infarction patients were selected.Plasma Hcy was measured by fluorescence polarization immunoassay(FPIA).Polymorphisms of the MTHFR gene were measured by polymerase chain reaction and restriction fragment length polymorphism(PCR-RFLP).Carotid arteries were detected by carotid ultrasonography in all patients.According to ultrasonography results,the patients were divided into plaque group having carotid atherosclerotic plaque and non-plaque group.The plasma Hcy levels and MTHFR gene polymorphism were compared between two groups.Results The frequencies of TT genotype(35.8% vs 17.0%) and T allele(58.6% vs 40.4%) were significantly higher in plaque group than in non-plaque group(P<0.05).Plasma Hcy levels was significantly higher in plaque group than in non-plaque group(22.42±11.04 μmol/L vs 17.89±5.96 μmol/L,P<0.05).The Hcy concentration was significantly higher in TT genotype than CT and CC genotypes(P<0.05).Logistic regression analysis adjusted for gender,age,hypertension,diabetes,hyperlipidemia,smoking,drinking and other risk factors,plasma Hcy levels of carotid atherosclerosis remained an independent risk factor for plaque(OR 1.160(95% CI 1.034～1.301),P<0.05).Conclusions Elevated Hcy levels was an independent risk factor for carotid artery plaques in cerebral infarction patients.MTHFR C677T polymorphism was significantly related to plasma Hcy levels.