The aim of the study was to assess the feasibility of metabonomics in clinical studies. A 1H nuclear magnetic resonance (NMR)-based metabonomic analysis was performed on plasma and urine samples obtained from a group of 12 healthy male subjects on two separate study days 14 days apart. The subjects were fed a standard diet and plasma and urine samples were obtained on both days. The 1H NMR spectra obtained for urine and plasma samples were analysed using principal components analysis (PCA) in order to generate metabonomic data. In plasma there was relatively little variability between subjects and study days. In the case of endogenous urinary metabolite profiles there was considerable inter-subject variability, but less intra-subject variation. In all subjects diurnal variation was seen with urine samples. This suggests the possibility to collect consistent metabonomics data in clinical studies.