It is uncertain whether the exposure to infections may decrease or increase the risk of allergy development in adult age. According to the hygiene hypothesis, an early childhood infection can down-regulate immunity, suppressing allergic and autoimmune disorders. Novel epidemiological data from a cross-sectional survey show that in subjects with active Helicobacter pylori infection the prevalence of asthma, eczema, allergic rhinitis is lower than in H. pylori-negative subjects. This information is supported by several mechanistic disease models, but is in contrast with previous reports on the association between H. pylori and atopic conditions. The public health relevance of both allergic disorders and H. pylori-related diseases calls for prospective and therapeutic studies. Studies able to show a cause-effect relationship are now essential to bring evidence that might make the case against H. pylori eradication in children and when such intervention is not highly recommended.