Introduction Amyotrophic lateral sclerosis (ALS) and Parkinson's disease (PD) are two severe neurodegenerative disorders for which the disease mechanisms are poorly understood and reliable biomarkers are absent. Objectives To identify metabolite biomarkers for ALS and PD, and to gain insights into which metabolic pathways are involved in disease. Methods Nuclear magnetic resonance (NMR) metabolomics was utilized to characterize the metabolite profiles of cerebrospinal fluid (CSF) and plasma from individuals in three age, gender, and sampling-date matched groups, comprising 22 ALS, 22 PD and 28 control subjects. Results Multivariate analysis of NMR data generated robust discriminatory models for separation of ALS from control subjects. ALS patients showed increased concentrations of several metabolites in both CSF and plasma, these are alanine (CSF fold change = 1.22, p = 0.005), creatine (CSF-fc = 1.17, p = 0.001), glucose (CSFfc = 1.11, p = 0.036), isoleucine (CSF-fc = 1.24, p = 0.002), and valine (CSF-fc = 1.17, p = 0.014). Additional metabolites in CSF (creatinine, dimethylamine and lactic acid) and plasma (acetic acid, glutamic acid, histidine, leucine, pyruvate and tyrosine) were also important for this discrimination. Similarly, panels of CSFmetabolites that discriminate PD from ALS and control subjects were identified. Conclusions The results for the ALS patients suggest an affected creatine/creatinine pathway and an altered branched chain amino acid (BCAA) metabolism, and suggest links to glucose and energy metabolism. Putative metabolic markers specific for ALS (e.g. creatinine and lactic acid) and PD (e.g. 3-hydroxyisovaleric acid and mannose) were identified, while several (e.g. creatine and BCAAs) were shared between ALS and PD, suggesting some overlap in metabolic alterations in these disorders. Keywords Amyotrophic lateral sclerosis (ALS) Á Parkinson's disease (PD) Á NMR metabolomics Á Biomarker Á Cerebrospinal fluid (CSF) Á Plasma Abbreviations ALS Amyotrophic lateral sclerosis PD Parkinson's disease NMR Nuclear magnetic resonance MS Mass spectrometry EDTA Ethylenediaminetetraacetic acid CSF Cerebrospinal fluid CPMG Carr-Purcell-Meiboom-Gill PCA Principal component analysis OPLS Orthogonal projection to latent structures DA Discriminant analysis EP Effect projection CV-ANOVA Analysis of variance testing of crossvalidated predictive residuals CNS Central nervous system BCAA Branched chain amino acids Electronic supplementary material The online version of this article (