To study the relation between host genetic background and the susceptibility to H.pylori associated gastric cancer, PCR-sequencing and PCR-RFLP were used to screen SECRETOR gene polymorphisms in 142 subjects including 69 cancer patients and 73 non-cancer individuals from high-risk area of gastric cancer in Shandong and 93 control individuals from Beijing. Results showed that the difference in se(w)/se(w) distribution between non-cancer individuals and Beijing population was significant (P<0.01,OR is 3.06,95% CI,1.28-7.30), but that between cancer patients and non-cancer individuals was not with significance. SE gene polymorphism was not relevant to H.pylori infection. We concluded that Shandong population from high-risk area of gastric cancer shared a high distribution of se(w)/se(w) genotype,which could be considered as one of the genetic markers.