IBD arises from complex interactions between a genetically altered intestinal immune response, environmental factors and intestinal microbiota. Disease phenotypes are heterogeneous and predicting individual disease course or therapy response is still merely possible; treatment of choice for instance remains a trial-and-error based succession of regimens. Further exploration of the underlying biologic mechanisms, and the identification and validation of non-invasive markers to predict disease course and therapy response are the foremost challenges in IBD field at this moment.