A large number of studies link infection with a reduced risk of developing extra-gastric conditions such as allergy, asthma, inflammatory bowel disease, coeliac disease and multiple sclerosis. The strength of the evidence for these protective associations is quite variable, and published studies often do not agree. This review article discusses some of the reasons for these discrepancies, and the difficulties faced when designing studies Examples of some protective disease associations are described in detail, where the evidence is most abundant and thought to be more reliable. The most convincing of these are supported by published mechanistic data, for example with animal models, or incidence of disease exacerbation in humans following eradication. Although controversial, this field is very important as the prevalence of is decreasing throughout the world whilst many chronic diseases are becoming more common. These trends are likely to continue in the future, therefore it is important that we fully understand if and how confers protection.