The incidence of inflammatory bowel disease, a relapsing intestinal condition whose precise etiology is still unclear, has continually increased over recent years. Metabolic profiling is an effective method with high sample throughput that can detect and identify potential biomarkers, and thus may be useful in investigating the pathogenesis of inflammatory bowel disease. In this study, using a metabonomics approach, a pilot study based on ultra-performance liquid chromatography coupled with electrospray ionization quadrupole time-of-flight mass spectrometry (UPLC-ESI-QTOF-MS) was performed to characterize the metabolic profile of plasma and urine samples of rats with experimental colitis induced by 2,4,6-trinitrobenzene sulfonic acid. Acquired metabolic profile data were processed by multivariate data analysis for differentiation and screening of potential biomarkers. Five metabolites were identified in urine: two tryptophan metabolites [4-(2-aminophenyl)-2,4-dioxobutanoic acid and 4,6-cihydroxyquinoline], two gut microbial metabolites (phenyl-acetylglycine and p-cresol glucuronide), and the bile acid 12a-hydroxy-3-oxocholadienic acid. Seven metabolites were identified in plasma: three members of the bile acid ⁄ alcohol group (cholic acid, 12a-hydroxy-3-oxocholadienic acid and cholestane-3,7,12,24,25-pentol) and four lysophosphatidylcholines [LysoPC(20:4), LysoPC(16:0), LysoPC(18:1) and LysoPC(18:0)]. These metabolites are associated with damage of the intestinal barrier function, microbiota homeostasis, immune modulation and the inflammatory response, and play important roles in the pathogenesis of inflammatory bowel disease. Our results positively support application of the metabonomic approach in study of the pathophysiological mechanism of inflammatory bowel disease.Abbreviations 5-HT, serotonin; DSS, dextran sodium sulfate; IBD, inflammatory bowel disease; LysoPC, lysophosphatidylcholine; MPO, myeloperoxidase; OPLS-DA, orthogonal projections to latent structures discriminant analysis; PCA, principal components analysis; TNBS, 2,4,6-trinitrobenzene sulfonic acid; UPLC-ESI-QTOF-MS, ultra-performance liquid chromatography coupled with electrospray ionization quadrupole time-of-flight mass spectrometry; VIP, variable importance in projection.