This chapter serves as a guide to gastrointestinal (GI) endoscopy for the histopathologist for benign pathology and outlines the value to endoscopists of GI biopsies. It sets out to explain to a histopathology audience the decision-making process that endoscopists undertake when performing an endoscopic procedure and, crucially, what they need in return in a pathology report. There are explanations as to the thought processes that lead to endoscopic biopsies both in macroscopic disease and, perhaps more importantly, when appearances are normal. There is a guide to each anatomical area detailing how, where, and when to take samples from each region from the oesophagus to the rectum, followed by detailed up-to-date explanations on the latest guidelines for endoscopic sampling for each disease state. For each anatomical area there are practice point summaries and for some diseases detailed endoscopic pictures. The goal of this chapter is to enhance the pathologist’s knowledge of endoscopy, benign GI disease, and national and international sampling guidelines. Finally, we hope it serves as a guide for enhanced discussion between endoscopists and pathologists and encourages a collaborative approach to disease diagnosis.

The small intestine has three structural parts: duodenum, jejunum and ileum. The jejunum and ileum are about 2.5 m long and 3 m long respectively in adults and form the majority of the small intestine, which has a total mucosal surface area of approximately 30 square metres. The small intestine was long regarded as a place where little happens, essentially because visualisation was imprecise or inaccurate. With the development of flexible endoscopy, it was possible first to reach the ileum because of ileocolonoscopy, and later to reach the jejunum because of enteroscopy. As a result of these developments, biopsies from the ileum and jejunum are now part of routine histopathological practice. The pathology may include neoplastic and inflammatory diseases. This chapter on jejunitis and ileitis focuses mainly on the inflammatory conditions. These can be limited to the small intestine, jejunum, and/or terminal ileum, or may also involve the upper gastrointestinal tract and/or colon and rectum. The text includes a description of both acute, usually infectious, diseases, and chronic inflammatory diseases. There are many chronic diseases, affecting in particular the terminal ileum. Clinically, Crohn’s disease is often a consideration. Drug-induced lesions, infections, endometriosis, ulcerative colitis, lymphoma, and lymphoid hyperplasia can mimic Crohn’s disease of the terminal ileum. Biopsies can help to solve the differential diagnosis and orient the clinical team towards proper management of the patient.