Crohn's disease and ulcerative colitis are two chronic relapsing inflammatory bowel diseases of unknown etiology. Both conditions are characterized by a considerable morbidity and have an impact upon the social and economic aspects of the patients life. At present, medical treatment is mainly aiming at the control of the inflammation. Drugs used for ulcerative colitis can induce microscopic healing of the mucosa. Similar results have been obtained recently with immunomodulatory drugs in Crohn's disease. The cost of these drugs is however high and the use of these drugs can be associated with side effects. Furthermore, many of the drugs need to be given for a long period. Therefore it is appropriate to assess the efficacy of the drugs before commercial use and even when used in routine practice. For both ulcerative colitis and Crohn's disease, clinical parameters combined in indices and endoscopy are commonly used together with some laboratory tests for the assessment of disease activity. In ulcerative colitis, histology has been used along with the other instruments for the measurement of disease activity because it was shown that the mucosal lesions could improve. More recently, histology has also been used for Crohn's disease. Routinely, disease activity when assessed with microscopy, should be divided into mild, moderate and severe. For drug trials and study purposes, more objective scoring systems should be used. Preferentially, a generally accepted score is used. This allows comparisons between different studies. Different scoring systems have been designed for ulcerative colitis and Crohn's disease. For the latter, multiple biopsies should be analysed. Most scoring systems still need validation.