Plasma obtained from three strains of Zucker rats was analysed using capillary gas chromatography/mass spectrometry (GC/MS) to obtain global metabolite profiles as part of a series of metabonomic investigations of animal models of diabetes. Samples were obtained from 20-week-old male wild-type Zucker lean, (fa/fa) obese and lean/(fa) animals and were analysed following protein precipitation, using acetonitrile, and derivatisation. Subsequent data analysis using principal components analysis (PCA) and orthogonal projection to latent structures (OPLS) revealed differences between the plasma metabolite profiles of the three strains, with those of the Zucker lean and the lean/(fa) crosses being similar to each other whilst differing from the (fa/fa) obese strain. Copyright © 2006 John Wiley & Sons, Ltd.