Metabolomic analysis has the potential to generate disease-specific metabolite signatures unique to individuals. Autoimmune illnesses, such as inflammatory uveitis, have highlighted the discriminative power of metabolomics by allowing disease sub-classification. Elucidating surrogate markers for neurological disease is particularly important, given the constraints in accessing central nervous system tissue in vivo. Metabolomic analysis, using either (1)H NMR spectroscopy or mass spectroscopy can be performed using biofluids such as urine, blood or cerebrospinal fluid and may permit the identification of disease specific metabolite signatures which may be useful as disease biomarkers. This is particularly relevant to complex diseases such as multiple sclerosis where promising preliminary work has been carried out. Future work in this field may well generate metabolite profiles to monitor disease evolution, prognosticate and guide therapeutic decisions.