Epidemiological and experimental data suggest that infections or the exposure to non-pathogenic bacteria protect individuals from developing some autoimmune and atopic disorders. Generally, these findings support the 'hygiene hypothesis', which attributes the rise in autoimmune and atopic disorders to a lack of infections that normally keep the immune system balanced by inducing immunoregulation. The suspected key players for infection-mediated immune suppression of autoimmunity and atopy are T regulatory cells and dendritic cells, which produce immunosuppressive cytokines, such as interleukin-10 and transforming growth factor-beta. However, there is also solid evidence suggesting that infections can exacerbate or even directly cause autoimmune and allergic disorders. In this Review, we discuss which type of infections induce, exacerbate or inhibit allergic and autoimmune diseases and point at infection-induced immunological mechanisms influencing the development of autoimmunity and atopy.