Treatment with nitrate, but not nitrite, improves exercise performance, in part, by increasing availability of metabolic fuels that require less oxygen for energy production. However, the mechanisms by which these inorganic anions produce performance effects is not well understood. PURPOSE: The purpose of this study is to quantify changes in the metabolic state in zebrafish muscle and liver with nitrate and nitrite treatment during exercise using gene expression and metabolomic methods. METHODS: Liver and muscle were collected from adult zebrafish fish exposed to sodium nitrate (606.9 mg NaNO3/L water), sodium nitrite (19.5 mg NaNO2/L of water), or control water for 21 days (n= 128-130). Tissues were analyzed by quantitative real-time PCR and 1H-NMR untargeted metabolomics. RESULTS: Nitrate treatment significantly increased expression of peroxisome proliferator activated receptor-γ (pparg), a gene involved in regulation of lipid and glucose metabolism. In contrast, acetyl-CoA carboxylase (acaca), a gene that inhibits fatty acid oxidation, significantly decreased in the skeletal muscle of fish treated with nitrate or nitrite as compared to control skeletal muscle tissue. Nitrite treatment also significantly increased carnitine palmitoyl transferase 1b (cpt1b) expression in the liver, which is a primary regulator involved in long-chain fatty acid transport into the mitochondria. Preliminary NMR results show that, relative to control skeletal muscle, nitrate treatment in unexercised fish at rest induces significant increases in metabolic fuels, such as ATP and creatine phosphate, and fuel sources including β-hydroxybutyrate and glycolytic intermediates. After a graded exercise test, the same metabolites increased in control but were decreased in skeletal muscle of nitrate-treated, exercised fish. CONCLUSIONS: Our data are consistent with the hypothesis that nitrate treatment may alter lipid and carbohydrate metabolism of zebrafish, in part, through a PPAR-γ mediated mechanism in the liver, and may improve exercise performance through utilization of fuel sources that require less oxygen during exercise. In contrast, our data indicate that nitrite may increase oxygen cost of exercise, in part, by promoting dependence on fatty acid oxidation in the liver of zebrafish.