Background: Crohn's disease and ulcerative colitis represent the 2 major phenotypes of inflammatory bowel disease (IBD) that are characterized by chronic inflammation of all or parts of the gastrointestinal tract. The pathogenesis of both diseases is influenced by genetic predispositions as well as microbial and environmental factors. Currently, there is an emerging consensus hypothesis that a microbial dysbiosis is involved in initiating the disease or in maintaining it. These compositional alterations may be reflected in altered metabolic activities of the gut microbiota and has led to the use of ‘omic' profiling to improve the understanding of the pathophysiology of IBD. Key Messages: In the past few years, a metabolic approach has increasingly been applied in a number of studies of experimental and human IBD which were mostly focused on exploring disease-related metabolites to gain more insight into metabolic pathways. Metabolomics involves the high throughput identification, characterization and quantification of small molecule metabolites by different analytical techniques and has been performed in different biofluids such as serum/plasma, urine or fecal samples. The application of such a metabolite profiling technique has revealed different metabolites that allow the discrimination of IBD patients from healthy controls. In addition, separate IBD subtypes could be differentiated. Some of these metabolic changes were directly associated to alterations of specific gut microbial populations, implying a perturbation in the gut microbiome in the development of IBD. Conclusions: This review covers the emerging contribution of metabolomics for the discovery of an IBD signature and to identify biomarkers linked with a metabolic imbalance. For the implementation of metabolomics as a diagnostic tool in IBD, large prospective cohort studies are necessary.