Aim To evaluate the relationship between 5A/6A polymorphism in the promoter of stromelysin-1 gene and cerebral thrombosis in Chinese population. Methods The stromelysin-1 promoter 5A/6A polymorphism in 1 122 patients with cerebral thrombosis and 1 123 controls were screened by polymerase chain reaction (PCR), and then corresponding probe hybridization was performed. Results The distribution of 5A/6A polymorphism was in agreement with Hardy-Weinberg Equilibrium in both patients and controls. The prevalence of 5A5A, 5A6A and 6A6A genotypes were 2.50%, 27.63% and 69.88% in patients, and 2.23%, 26.18% 71.59% in controls, respectively. No significant difference was observed between these two groups (p>0.05). The 5A allele frequencies were 16.31% in patients, and 15.32% in controls. There is no dramatic distinction between cases and controls, either (p>0.05). Conclusion 5A/6A polymorphism in the promoter of stromelysin-1 gene is not a genetic marker of cerebral thrombosis in Chinese population.