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This study assessed the hypothesis that Helicobacter pylori infection and specific living conditions in childhood are associated with allergic outcomes. A cross-sectional survey containing retrospective questions concerning childhood was performed in an occupational population in 2001. This survey included self-administered questionnaire data and stool tests. An inverse association between positive H. pylori infection status and physician diagnosis of allergy/12 month period of anti-allergic medication was observed in a logistic regression model, adjusted for potential confounders (age, sex, nationality, smoking status and education of the participant) (OR 0.26, 95% CI: 0.08–0.84). In addition, childhood living conditions were associated with H. pylori infection status and signs of allergies. In line with the “hygiene hypothesis” our model supports an inverse association between early childhood infection with H. pylori and allergic disease in adulthood.