Objective To investigate the association of the polymorphism of the cystathionine β synthase (CBS) T833C, CBS 844ins68 and cerebral arterial thrombosis in Chinese population. Methods We electronically searched CBM, CNKI, Wanfang database, VIP and PubMed from 1999 to February 2010 to collect case studies on CBS polymorphism and cerebral arterial thrombosis of the Chinese. We evaluated the quality of the included studies and the extracted data. RevMan 4.2 was used for meta-analyses. Results We identified 4 case-control studies on association of CBS T833 polymorphism and cerebral arterial thrombosis of the Chinese. In Shandong subgroup, the Chinese people with TC+CC genotypes of T833C had higher risk of cerebral arterial thrombosis at OR 5.01 and 95%CI 2.63 to 9.53 (Plt;0.000 01). In non-Shandong subgroup, higher risk of cerebral arterial thrombosis was found in the Chinese people with genotype of CT+CC at OR 0.95 and 95%CI 0.60 to 1.50 (P=0.82). Meta-analyses of the 4 case studies showed there were no significant differences in the risk of cerebral arterial thrombosis between people with genotype of DI and II and people with genotype of DD at OR 1.20 and 95%CI 0.72 to 1.99 (P=0.49). Conclusion Our findings suggest that in Chinese population, CBS T833C polymorphisms might be associated with cerebral arterial thrombosis in Shandong subgroup; 844ins68 polymorphisms does not increase the risk of cerebral arterial thrombosis for the Chinese.