OBJECTIVE To study the association of plasma homocysteine (Hcy) and polymorphism and cystathionine beta-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 l5.28 micromol/L (95% CI 14.37-16.19 micromol/L) in the patient group, higher than that in the control group (11.32 micromol/L, 95% C1 10.47-12.16 micromol/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). CONCLUSIONS 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.