The application of HPLC-MS combined with principal components analysis (PCA) to the metabonomic analysis of mouse urine is demonstrated. Urine samples from three strains of mouse were analysed by gradient HPLC-MS combined with positive and negative electrospray time-of-flight mass spectrometry. Analysis of the resulting data using PCA enabled the samples to be discriminated between on the basis of gender, strain and diurnal variation. These preliminary results suggest that HPLC-MS-based approaches may have a useful role in metabonomic analysis that complements existing approaches.