Objective To explore the effect of homocysteine(Hcy) on the prognosis of coronary artery heart disease(CHD) and stroke. Methods Totally 234 patients with CHD or stroke were divided into control group and folic acid-therapy group randomly. Patients in control group were comprehensively treated with antihypertensive, lipid-adjusting, hypoglycemic and anti-platelet aggregation drugs, while patients in folic acid-therapy group were given oral folic acid tablets(10 mg per day) besides above treatment. Period of treatment was one year and patients were all followed up. Plasma Hcy levels were measured prior treatment, 6 months and 12 months post treatment and the incidences of clinical event with coronary artery heart disease(acute left heart failure, acute myocardial infarction, sudden cardiac death, angina pectoris attack and arrhythmia) and stroke(apoplexy, transient ischemic attack or reversible ischemic injury, cerebral hemorrhage) were also monitored. Results There was no significant difference in plasma, Hcy between control group and folic acid-therapy group at prior treatment and 6 months post treatment(P＞0.05). However, 12 months after treatment plasma, Hcy level in folic acid-therapy group was significantly lower than that in control group(P＜0.05). The incidences of clinical event with CHD and stroke were 11.02% and 26.92% respectively in control and olic acid-therapy group 12 months after treatment (P＜0.05). Logistic regression analysis showed that the incidences of clinical event with CHD and stroke were related with diabetes mellitus and Hcy (P＜0.05, P＜0.01); moreover, Hcy was a risk factor of CHD and Stroke. Conclusion Hcy is significantly correlated to clinical event with CHD and stroke; oral administration of folic acid can significantly decrease the incidence of clinical event with CHD and stroke through reducing plasma Hcy level and has great function in the secondary prevention of CHD and stroke.