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The primary objective of this study was to determine and characterize surrogate biomarkers that can predict nephrotoxicity induced by mercuric chloride (HgCl2) using urinary proton nuclear magnetic resonance (1H NMR) spectral data. A procedure for 1H NMR urinalysis using pattern recognition was proposed to evaluate nephrotoxicity induced by HgCl2 in Sprague–Dawley rats. HgCl2 at 0.1 or 0.75 mg/kg was administered intraperitoneally (i.p.), and urine was collected every 24 h for 6 days. Animals (n = 6 per group) were sacrificed 3 or 6 days post-dosing in order to perform clinical blood chemistry tests and histopathologic examinations. Urinary 1H NMR spectroscopy revealed apparent differential clustering between the control and HgCl2 treatment groups as evidenced by principal component analysis (PCA) and partial least square (PLS)-discriminant analysis (DA). Time- and dose-dependent separation of HgCl2-treated animals from controls was observed by PCA of 1H NMR spectral data. In HgCl2-treated rats, the concentrations of endogenous urinary metabolites of glucose, acetate, alanine, lactate, succinate, and ethanol were significantly increased, whereas the concentrations of 2-oxoglutarate, allantoin, citrate, formate, taurine, and hippurate were significantly decreased. These endogenous metabolites were selected as putative biomarkers for HgCl2-induced nephrotoxicity. A dose response was observed in concentrations of lactate, acetate, succinate, and ethanol, where severe disruption of the concentrations of 2-oxoglutarate, citrate, formate, glucose, and taurine was observed at the higher dose (0.75 mg/kg) of HgCl2. Correlation of urinary 1H NMR PLS-DA data with renal histopathologic changes suggests that 1H NMR urinalysis can be used to predict or screen for HgCl2-induced nephrotoxicity.