Aim To observe the level of the serum cystatin C and β2-microglobulin of acute cerebral infarction patients and its relationship with different subtypes by the Trial of Org10172 in Acute Stroke Treatment (TOAST). Methods The investment contains 115 acute cerebral infarction patients and 50 controls ,and the patients were classified into five subtypes according to TOAST creteria . Recorded the serum Cyst-C and β2-MG level and analyzed the difference between the two groups and their TOAST subtypes. Results The serum Cyst-C and β2-MG of the patients was significantly higher than the controls(P ＜ 0.05). Logistic linear regression analysis showed that serum level of Cyst-C had significant correlation(P ＜ 0.05). The serum Cyst-C of the subtypes was significantly higher compared to the controls,and the level of Cyst-C in the CE was the highest (P ＜ 0.05). There was no difference among each subtypes of the serumβ2-MG. Logistic linear regression analysis showed that serum level of Cyst-C had significant correlation with CE (OR=8.98;95% CI 1.051-8.677 ). Conclusion The changes in the levels of serum Cyst-C, beta 2-MG may be risk factor of cerebral infarction. The serum Cyst-C varied with different subtypes of cerebral infarction,specially elevating in the subtype of CE,which indicates that the serum Cyst-C is possibly connected with etiology of cerebral infarction.