Endoscopic evaluation and mucosal biopsy analysis have assumed important roles in the clinical management of patients with symptoms related to the gastrointestinal tract. Several common inflammatory diseases, including eosinophilic esophagitis, Barrett's esophagus, Helicobacter pylori infection, celiac disease, lymphocytic colitis, collagenous colitis, and inflammatory bowel disease, may display a patchy or discontinuous distribution and, thus, multiple mucosal samples may be required to obtain diagnostic tissue in some cases. Not surprisingly, clinicians and pathologists are increasingly challenged to determine the optimum number of procedures and tissue samples necessary to detect, or exclude, the presence of inflammatory disorders of the gastrointestinal tract. Unfortunately, clinical practice varies widely with respect to tissue sample procurement in the evaluation of these disorders, particularly when the endoscopic appearance of the gastrointestinal mucosa is normal or shows only minimal changes. Guidelines concerning the appropriate number of tissue samples are well established for some diseases, such as Barrett's esophagus and chronic gastritis, but are not clear in other instances. The purpose of this review is to discuss the available literature pertaining to appropriate endoscopic sampling in the assessment of medical diseases of the gastrointestinal tract, and to develop recommendations regarding the clinical evaluation of common gastrointestinal disorders.