Recent studies have suggested that decrease in Helicobacter pylori infection may predispose to allergic diseases. However, there are few reports of the relationships of eosinophilic gastrointestinal disorders (EGIDs), especially eosinophilic gastroenteritis (EGE), with H. pylori infection. We investigated the possible influence of H. pylori infection on EGIDs in Japanese patients. We performed a case-control study to investigate the prevalence of H. pylori infection in patients with EGIDs. Eighteen with eosinophilic esophagitis (EoE) and 22 with EGE were enrolled. For each patient, 3 age- and gender-matched normal controls (n = 120) were randomly selected from a population who received a medical check-up between April 2010 and December 2011 at the Shimane Institute of Health Science. The mean ages of the EoE and EGE patients were 50.9 ± 17 and 49.2 ± 20 years, respectively. Males were more frequently seen in the EoE group, while there was no significant gender difference in regard to EGE. Of the patients with EoE, 22.3% were infected with H. pylori, as compared to 55.5% of their age- and sex-matched normal controls. The odds ratio for EoE patients to have an H. pylori infection was 0.22 (p<0.05). In addition, 22.7% of the patients with EGE and 48.5% of their matched controls were infected with H. pylori, with odds ratio for EGE patients to have an H. pylori infection shown to be 0.31 (p<0.05). In conclusion, the prevalence of H. pylori infection was significantly lower in EGE and EoE patients in Japan as compared to normal control subjects.