Autoimmunity can be triggered by many environmental factors, among which infectious agents are pivotal. Here, we summarize current knowledge of the relationship between infection and autoimmunity. An autoimmune disease can be induced or triggered by infectious agents, which can also determine its clinical manifestations. Most infectious agents, such as viruses, bacteria and parasites, can induce autoimmunity via different mechanisms. In many cases, it is not a single infection but rather the 'burden of infections' from childhood that is responsible for the induction of autoimmunity. The development of an autoimmune disease after infection tends to occur in genetically susceptible individuals. By contrast, some infections can protect individuals from specific autoimmune diseases (i.e. the hygiene hypothesis).