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Auto-antibodies that bind to conformational extracellular epitopes of neuronal receptors or synaptic proteins have provided clinicians with essential biomarkers in acute neurology. This review summarizes the current status and challenges in the field.In children, anti-N-methyl-D-aspartate receptor encephalitis remains the most identifiable autoimmune encephalitis, although many patients have a clinical syndrome of brain inflammation in which no antibodies are identified. Anti-myelin oligodendrocyte glycoprotein antibody associated demyelination is now recognized as a major cause of monophasic and relapsing demyelination, often presenting with encephalopathy. We discuss the importance of auto-antibody detection methodology and the possible influence of intrathecal antibody synthesis on the speed of recovery and response to immune therapy. The current, often pragmatic rather than evidence-based therapeutic pathway will be discussed, highlighting key challenges such as the timing of second-line therapy, monitoring of disease activity, and identifying the patient who is responding poorly to treatment.Although there have been significant developments, future priorities include the need for paediatric-specific consensus definitions for seronegative suspected autoimmune encephalitis, novel tools for monitoring patients with autoimmune encephalitis, consensus treatment recommendations, and neuroprotective strategies.