The model nephrotoxin cyclosporin A was administered to male Wistar-derived rats daily for 9 days at a dose level of 45 mg/kg per day. Urine samples were collected daily and the excretion pattern of low molecular mass organic molecules in the urine was studied using 1H NMR spectroscopy and HPLC-TOF/MS. Distinct changes in the pattern of endogenous metabolites, as a result of the daily administration of cyclosporin A, were observed by 1H NMR from day 7 onwards. The NMR-detected markers included raised concentrations of glucose, acetate, trimethylamine and succinate and reduced amounts of trimethylamine-N-oxide. In parallel studies by HPLC-TOF/MS a reduction in the quantities of kynurenic acid, xanthurenic acid, citric acid and riboflavin present in the urines was noted, together with reductions in a number of as yet unidentified compounds. In addition, signals resulting from the polyethylene glycol, present in the dosing vehicle, and cyclosporin A metabolites were detected by MS. However, these were excluded from the subsequent multivariate data analysis in order to highlight only changes to the endogenous metabolites. Analysis of both the 1H NMR and HPLC-MS spectroscopic data using pattern recognition techniques clearly identified the onset of changes due to nephrotoxicity.