Chronic inflammatory bowel diseases (i.e., ulcerative colitis and Crohn's disease) are syndromes in which standardized criteria are necessary in the diagnostic process. The present review is based on the diagnostic criteria used at our institution. We base the diagnosis of ulcerative colitis and Crohn's disease on combined information from the patient history, and radiological, endoscopic and histological findings after exclusion of neoplastic and infectious disease. The patient history must include precise information on the nature and duration of symptoms as well as the presence of relevant influential factors such as travel activity, drug intake and sexual habits. In immunocompromised patients extensive microbiological investigations are required to exclude infection. Typical radiological and colonoscopic findings in ulcerative colitis are mucosal inflammatory changes extending circumferentially and continuously from the rectum and proximally in the colon. In contrast, Crohn's disease is most frequently located in the small bowel and in case of colonic involvement, the rectum is often spared. The best predictors of Crohn's disease are discontinuous lesions, cobblestones and apthous ulceration. Histological changes such as abnormal mucosal architecture and lamina propria cellularity, neutrophil polymorph infiltration and epithelial cell abnormality are useful and reproducible features in the evaluation of colorectal biopsy specimens. The inflammatory bowel diseases, ulcerative colitis and Crohn's disease, continue to be etiological and diagnostic challenges. Increased use of standardized criteria and diagnostic algorithms are essential instruments to improve the overall quality of the management of patients with these diseases.