The development of an approach by which two CE methods operating with opposite polarities and orthogonal capillary electrophoretic separation modes (method 1: normal polarity cyclodextrin modified MEKC (CD-MEKC) and method 2: reversed polarity CZE) for the sequential application to urinary samples from a type I diabetes metabolomics investigation is discussed. During method development, problematic MEKC profile drift issues arising from the high glucose content of the diabetic animal urine samples required some electrolyte modifications involving the use of hexafluoroisopropanol (HFIP) to circumvent the drift. Data derived from both methods were subsequently subjected to alignment, normalization and multi-dimensional scaling (MDS) procedures. In such a way, classification of samples derived from control and diabetic animals receiving a placebo from those receiving an antioxidant nutraceutical, was successfully demonstrated. Such a strategy is a cost effective and comprehensive metabolomics tool useful for describing UV absorbing metabolite disease-related changes in nutra/pharma-ceutical studies.