The development of flexible endoscopes has led to a great increase in the examination and mucosal biopsy evaluation of all portions of the large intestine and rectum. Examinations are now performed not only for the determination of diagnosis but also for the monitoring of the course of a wide variety of conditions and for the early detection of complications. This review concentrates on the uses and interpretations of such biopsies in a large number of inflammatory conditions, with special emphasis on the correlations with clinical and functional features. Illustrated are examples of infections, idiopathic inflammatory bowel disease (IBD), vascular disorders, motor and mechanical conditions, toxic and physical reactions, and other inflammatory conditions. Mucosal biopsy specimens also are obtained to identify dysplasia and to evaluate mass lesions, and these subjects are well covered in other articles within this symposium. In patients with chronic disorders multiple examinations are now expected to follow the course of the disease and to detect and correct any complications at an early stage. The exact reasons for the endoscopy and relevant clinical data are essential for the optimal analysis of these mucosal biopsy specimens.