Approximately 3.6 million people in Europe and the USA suffer from recurrent auto-immune-mediated inflammation of the gastrointestinal tract. Inflammatory bowel disease (IBD) comprises two entities: Crohn's disease (CD) and ulcerative colitis (UC). In the past, experimental studies (mostly in mice) have improved our understanding of the aberrant interaction between the intestinal microbiota and the immune system. The perturbed immune reaction in IBD exhibits specific and individual cytokine responses that distinguish the two variants. A deep understanding of the immunological response at every stage of the chronic disease enables the provision of modern, efficient medical treatment that takes into account individual immunological and genetic characteristics. In this review, the current knowledge on the epidemiology and genetics of IBD is summarized, and new pathogenetic insights as well as promising future therapeutic options are described.