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BackgroundFunctional dyspepsia (FD) is a multifactorial disorder. Helicobacter pylori (H. pylori)‐related dyspepsia (HpD) may be considered a separate entity. Duodenal eosinophilia is a potential pathogenic mechanism in FD. However, the impact of duodenal eosinophilia and host genetic polymorphism of innate and pro‐inflammatory cascade, nucleotide‐binding oligomerization domain 1 (NOD‐1), and interleukin‐1 beta (IL‐1β) in HpD was not explored.AimTo evaluate the association of NOD1‐796G>A and IL‐1B‐511C>T gene variants and low‐grade duodenal eosinophilia in HpD.MethodsA multicenter cross‐sectional study was conducted. A total of 253 patients who met Rome‐IV criteria were selected before upper endoscopy and 98 patients were included after unremarkable upper endoscopy and positive H. pylori in gastric biopsies were assessed. Clinical parameters, H. pylori cagA and duodenal histology, were evaluated.ResultsSixty‐four (65%) patients had epigastric pain syndrome (EPS), 24 (25%) postprandial distress syndrome (PDS), and 10 (10%) EPS/PDS overlap. FD subtypes were not associated with NOD1‐796G>A and IL‐1B‐511C>T gene variants. Low‐grade duodenal eosinophilia was significantly increased in NOD1‐796 GG versus single A‐allele, but not in IL‐1B‐511 single T‐allele or CC‐allele. This association is dependent of cagA infection, since harboring cagA strain was significantly associated with low‐grade duodenal eosinophilia with isolated variants NOD1‐796 GG and IL‐1B‐511 single T‐allele, but not without cagA. When we performed combined polymorphism analysis with NOD1‐796 GG/IL‐1B‐511 single T‐allele, a synergistic effect on low‐grade duodenal eosinophilia was found between these two loci irrespective of cagA strain status in HpD.ConclusionOur findings suggest that low‐grade duodenal eosinophilia is significantly associated with NOD1‐796 GG allele specially in cagA strain and with allelic combination NOD1‐796 GG/IL‐1B‐511 single T‐allele independent of cagA strain infection in HpD patients.