Evidence has linked genetic predisposition and environmental exposures to the worldwide pandemic of inflammatory bowel diseases (IBD), but underlying biochemical events remain largely undefined. Here, we studied the gradual development of colitis in Interleukin 10 deficient mice using a combination of (i) histopathological analysis of intestinal sections, (ii) metabolic profiling of blood plasma, and (iii) measurement of plasma inflammatory biomarkers. Data integration using chemometric tools, including Independent Component Analysis, provided a new strategy for measuring and mapping the metabolic effects associated with the development of intestinal inflammation at the age of 1, 8, 16, and 24 weeks. Chronic inflammation appeared at 8 weeks and onward, and was associated with altered cecum and colon morphologies and increased inflammatory cell infiltration into the mucosa and the submucosa. Blood plasma profiles provided additional evidence of loss of energy homeostasis, impaired metabolism of lipoproteins and glycosylated proteins. In particular, IL-10-/-mice were characterized by decreased levels of VLDL and increased concentrations of LDL and polyunsaturated fatty acids, which are related to the etiology of IBD. Moreover, higher levels of lactate, pyruvate, citrate and lowered glucose suggested increased fatty acid oxidation and glycolysis, while higher levels of free amino acids reflected muscle atrophy, breakdown of proteins and interconversions of amino acids to produce energy. These integrated system investigations demonstrate the potential of metabonomics for investigating the mechanistic basis of IBD, and it will provide novel avenues for management of IBD.