Several important advances have been made over the past few years that have expanded our knowledge of the immunology of the gut and its complex interactions with commensal organisms. Critical developments in our understanding of the pathogenesis of inflammatory bowel diseases include the discovery of Toll-like receptors and the identification of not one but two susceptibility genes for Crohn's disease. We have furthered our understanding significantly concerning the role of dendritic cells in the development of gut inflammation. In addition, a novel hypothesis suggesting a protective role for helminthic infections is gaining experimental evidence and direct clinical applicability. In this review we summarize these key developments in the pathophysiology of inflammatory bowel disease and attempt to ascribe clinical relevance where applicable.