Inflammatory bowel diseases (IBD) are idiopathic, chronic and relapsing inflammatory conditions of the gastrointestinal tract. New insights into the pathogenesis of IBD have been provided by three lines of research: (1) studying susceptibility genes involved in the detection of bacterial components and in the regulation of the host immune response, (2) highlighting the disruption of tolerance towards the commensal microbiota and (3) unravelling the critical role of environmental factors such as sanitation and hygiene. This review presents current etiological hypothesis of IBD which argue that pathogenic intestinal bacteria and/or infectious agents initiate and perpetuate the inflammation of the gut in an individual with genetic vulnerability leading to impaired epithelial barrier function and abnormal mucosal immune responses.