Abstract: Objective To study the association of plasma homocysteine (Hcy) and polymorphism and cystathionine β-synthase (CBS) with cerebral thrombosis.Methods Eighty-seven patients with first-ever acute cerebral thrombosis and 80 control subjects were examined for plasma Hcy levels using high-performance liquid chromatography-fluorescence detection and for CBS polymorphism determined by amplification refractory mutation system.Results The fasting plasma Hcy level was l5.28µmol/L (95% CI 14.37-16.19µmol/L) in the patient group, higher than that in the control group (11.32 μmol/L, 95% C1 10.47-12.16µmol/L, P<0.001). Plasma Hcy levels varied with different genotypes. No difference in genotype or allele frequencies was noted between patient group and control group (P>0.05).Conclusion Common mutations in CBS G919A and CBS T833C lead to hyperhomocysteinemia, which, instead of common mutations in CBS, is more directly associated with increased risk of cerebral thrombosis.