Inflammatory bowel disease (IBD) is a chronic inflammatory condition of unknown etiology that can develop in any portion of the digestive tract but which has a high incidence especially in the terminal ileum and/or in the colon. The diagnosis and management of IBD, including Crohn's disease (CD) and ulcerative colitis (UC), is still challenging, and the presence of intestinal inflammation is, to date, a primary criterion for its diagnosis and differentiation from other diseases. Moreover, there is no decisive gold standard diagnostic test based on patient history and physical examination, supplemented with objective laboratory, radiological, endoscopic and histological findings.This study analyzed plasma proteins and fatty acids using mass spectrometry-based techniques. Quantitation of low-abundance plasma proteins was performed by depleting 14 high-abundance proteins, followed by tryptic digestion and LC-MS analysis, while fatty acids were analyzed using GC-MS.We used bioinformatic tools to identify several new potential biomarkers for an early and non-invasive diagnosis of IBD, and to differentiate CD from UC. Moreover, the diagnostic power of the MS-identified biomarkers was also corroborated by Western Blot and ELISA assays. Hence, we identified the biological functions and pathways involved in the various subsets of IBD.Coagulation, fibrinolysis and acute phase response processes were found to be strongly involved in the condition. The involvement of several fatty acids, such as anti-inflammatory mediators, was also identified. Finally, proteomic and lipidomic data were integrated by using combinatorial and multivariate analyses to discover new combined biomarkers and to study the molecular pathways involved in IBD.