Hepatic encephalopathy (HE) is a severe complication of chronic liver disease (CLD). Treatments for HE have focused on reducing plasma ammonia levels implicated in HE pathogenesis. The antibiotic rifaximin reduces the production of gut ammonia which is considered to be the main toxin in CLD-induced HE. Rifaximin is commonly used in the treatment of HE and has been shown to reduce the frequency of HE episodes, but the molecular mechanisms behind this effect are unknown. We assessed, in vivo and longitudinally, the effect of rifaximin on brain metabolites in bile duct ligated rats using high-field proton Magnetic Resonance Spectroscopy.