Humans and the many parasites that we can host have co-evolved over millions of years. This has been compared to an arms race in which the immune armoury of the human has evolved to deal with potential pathogens and the pathogen has evolved strategies to evade, and in some cases use, the immune system of the human host. Recently, there have been marked changes in the exposure of individuals in the developed world to both microorganisms and metazoan parasites, so the immune stimuli such organisms provide no longer have a role in our lives. As we discuss here, this is a marked perturbation, and the absence of the associated immunomodulation might have led to the increased emergence of autoimmune diseases.