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Background and Aim: Toll-like receptor (TLR) 2 and TLR4 are cell surface signaling receptors that are involved in the recognition of and host response to Helicobacter pylori. Our aim was to investigate the association between TLR gene polymorphisms and susceptibility of Japanese subjects to 4 H. pylori-related gastrointestinal diseases. Methodology: A total of 100 patients with histologically diagnosed gastric cancer, 105 patients with gastric ulcer, 102 with atrophic gastritis, 72 with duodenal ulcer and 428 healthy controls were recruited. A TaqMan assay was used to genotype 7 single nucleotide polymorphisms (SNPs) in TLR2 and 6 SNPs in TLR4. Results: There was a tendency for TLR4 rs10759932 TC/CC genotypes to be associated with a decreased risk of gastric cancer (p = 0.059); however, this did not reach statistical significance. No significant associations were found between polymorphisms in TLR2 or TLR4 and the risks for gastric cancer, gastric ulcer, duodenal ulcer, or atrophic gastritis. Conclusion: The 13 SNPs inTLR2 and TLR4 examined in this study may not be linked with the development of H. pylori-related gastrointestinal diseases. Further studies with larger numbers of subjects are necessary to verify the present findings.