These studies were structured with the aim of utilizing emerging technologies in 2-D gel electrophoresis and mass spectrometry to evaluate protein expression changes associated with type I diabetes. We reasoned that a broad examination of diabetic tissues at the protein level might open up novel avenues of investigation of the metabolic and signaling pathways that are adversely affected in type 1 diabetes. This study compared the protein expression of the liver, heart, and skeletal muscle of diabetic prone rats and matched controls utilizing semi-quantitative liquid chromatography mass spectrometry and differential in gel 2-D gel electrophoresis. Differential expression of 341proteins in liver, 43 in heart and 9 (2D gel only) in skeletal muscle were detected. These data were assembled into the relevant metabolic pathways affected primarily in liver. Multiple covalent modifications were also apparent in 2-D gel analysis. Several new hypotheses were generated by these data including mechanism of net cytosolic protein oxidation, formaldehyde generation by the methionine cycle, and inhibition of carbon substrate oxidation via reduction in citrate synthase and short chain acyl CoA dehydrogenase.