Background Amyotrophic lateral sclerosis (ALS), an invariably fatal neurological disorder shows complicated pathogenesis that poses challenges with respect to diagnosis as well as monitoring of disease progression. Methods We investigated metabolite profiles in the serum of 30 patients with ALS, 10 patients of Hirayama disease, which served as a neurological disease control and 25 healthy controls by using (1) H NMR spectroscopy. Results Compared to healthy controls, the ALS patients had higher quantities of glutamate ( P < 0.001), beta-hydroxybutyrate ( P < 0.001), acetate ( P < 0.01), acetone ( P < 0.05), and formate ( P < 0.001), and lower concentrations of glutamine ( P < 0.02), histidine ( P < 0.001) and N-acetyl derivatives. On the other hand, Hirayama disease patients had significantly higher median concentrations of pyruvate ( P < 0.05), glutamate ( P < 0.001), formate ( P < 0.05) and lower median concentrations of N-acetyl derivatives. Furthermore, we also found that serum glutamate showed a positive correlation ( P < 0.001, r = 0.6487) whereas, histidine showed a negative correlation ( P < 0.001, r = − 0.5641) with the duration of the disease in ALS. Conclusions Such (1) H NMR study of serum may reveal abnormal metabolite patterns, which could have the potential to serve as surrogate markers for monitoring ALS disease progression.