There is a wealth of experimental information and some clinical evidence available in the literature suggesting that taurine exerts preventive effects on cardiovascular diseases. In particular, taurine has been shown to reduce blood pressure in not only hypertensive patients but also in a number of hypertensive rodent models such as spontaneously hypertensive rats (SHR). However, the molecular basis of the efficacy and toxicity of the compound has not been fully characterized. We have investigated the effects of taurine supplementation to urinary low-molecular-weight endogenous metabolites in SHR using a (1)H NMR-based urinary metabonomic approach. The SHR were chronically treated with 3% taurine in drinking water from four to 14 weeks of age, and 24-h urine samples were analyzed using (1)H NMR spectroscopy. Metabolic information was extracted from the NMR data by principal components analysis as well as visual inspection. Consequently, the metabolite profile started to change with considerable interindividual variation from six weeks of age. The extent of change became increasingly remarkable with the duration of treatment, with the concurrent observation of the hypotensive effect. The metabolic changes included a decreased urinary output of tricarboxylic acid cycle intermediates (citrate, α-ketoglutarate, and succinate) and an increased output of phenylacetylglycine and p-cresol sulfate. The results suggest that chronic taurine supplementation to the SHR resulted in an acceleration of metabolic acidosis with perturbation in the tricarboxylic acid cycle and the modulation of the intestinal microbial metabolism.