Inflammatory bowel disease, with Crohn's disease and ulcerative colitis as the two main disorders, is a heterogeneous group of disorders of unknown etiology. Clinical initial presentation is sometimes misleading and causing diagnostic delay which may be important. Identification of subgroups of patients on the basis of genetic, immunologic and clinical markers will be important for exact diagnosis, but also for new drug trials. The current diagnosis depends on clinical, radiographic, endoscopic and laboratory data. The introduction of serological markers such as pANCA and ASCA will allow an increase in the diagnostic accuracy at initial diagnosis of inflammatory bowel disease and may play a role in defining subgroups of the disease.