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Inflammatory and auto-immune disorders of the central nervous system are a heterogeneous group of disorders. Many of these disorders are potentially treatable with immune therapies that can reduce disability or prevent death. We review the clinical value of biomarkers which can aid in the diagnosis of paediatric inflammatory and auto-immune central nervous system (CNS) disorders.This review will first describe the clinical usefulness of nonspecific biomarkers of CNS inflammation such as cerebrospinal fluid neopterin and oligoclonal bands. Neopterin is produced by immune and neuronal cells after stimulation by interferon species and is increased in a broad range of inflammatory and auto-immune CNS disorders. Oligoclonal bands represent clonal production of immunoglobulin G in the CNS and are present in demyelinating, auto-immune, and infectious CNS disorders. In addition, we will review new advances in the immunogenetic investigation of familial auto-inflammatory disorders such as Aicardi-Goutières syndrome and Chronic Infantile Neurologic Cutaneous Articular syndrome. Finally, we will review the clinical utility of auto-antibodies in CNS disorders, with specific focus on auto-antibodies that bind to cell surface proteins such as N-methyl-D-asparate receptor, voltage-gated potassium channels, myelin oligodendrocyte glycoprotein, and aquaporin-4.These biomarkers are increasingly important in the recognition and treatment of inflammatory and auto-immune CNS disorders. Like many biomarkers in paediatric practice, it is essential to interpret the findings in the context of the patient history and examination.