NMR-based metabolomics of saliva was studied in patients with Parkinson’s disease (PD) in early and advanced stages in comparison with that of healthy controls (HC). Higher levels of histidine, TMAO, propionate, GABA, valine, isoleucine, alanine, and fucose were observed in early PD in comparison with HC. Higher propionate and acetoin concentrations were observed in both early and advanced PD groups as compared to the HC group. An association of a few metabolites with the disease duration, LEDD and H&Y stage of PD patients was observed. Gut microflora system, ketone body and energy metabolisms may be impaired in patients with PD.