Objective To explore the relationship between the single nucleotide polymorphisms(SNPs) of IVS13-98G/T of human protection of telomeres 1(hPOT1) genes and H.pylori infection.Methods A total of 150 cases of gastric carcinoma and 156 cancer-free controls were genotyped by polymerase chain reaction(PCR) and PCR-restriction fragment length polymorphism(PCR-RFLP) method.H.pylori was identified with PCR and Warthin-Starry methods.Results The frequencies of GG,GT,and TT genotypes of hPOT1IVS13-98 G/T were 22.00%,41.67% and 36.67% in patients and 24.36%,51.92%,and 23.72% in controls,respectively.The OR for any GT and GG genotype was 0.432(95% CI: 0.242-0.772,P=0.005) and 0.540(95% CI: 0.274-1.064,P=0.075) when compared with TT genotype,respectively.There were no differences in genotype distribution and allele frequency of IVS13-98 G/T polymorphism(?2=3.0257,P= 0.0820).hPOT1IVS13-98 G/T polymorphism was not correlated with H.pylori infection in gastric cancer.Conclusion Our results indicated that IVS13-98 G/T SNP of hPOT1 gene might be associated with reduced risk for gastric carcinoma,but not with H.pylori infection.