Autoimmune diseases affecting the CNS can be part of a systemic disease, such as systemic lupus erythematosus, or an exclusive neurological disorder, such as multiple sclerosis. While the clinical phenotypes show some overlap, the underlying pathophysiological mechanisms diverge in each condition. The rarity of these dysimmune diseases in paediatrics implies the effectiveness, or immaturity, of the immune system in preventing or rectifying autoimmune reactions induced by various environmental agents. However, when such diseases commence in this age group, they show a particularly inflammatory course which warrants the awareness of their diagnostic criteria and underlying mechanisms, to ensure prompt and appropriate treatment.