Most infections that involve the small bowel are self-limiting, and endoscopic examination is rarely indicated in these cases. Suspicion of microbial enteritis can be confirmed by stool cultures and, if necessary, by detection of toxins, antigens, or by polymerase chain reaction (PCR) assay. Persistent diarrhea and associated symptoms such as weight loss, fever, arthralgia, and neurologic deficits or findings such as anemia, inflammatory signs, eosinophilia, or signs of malabsorption warrant further investigation. Besides microscopic stool examination, the main tool for this purpose is flexible endoscopy with tissue sampling from the duodenum, terminal ileum, and colon. Small bowel capsule endoscopy (SBCE) can sometimes reveal changes in the jejunum or ileum, having a high negative predictive value to exclude such lesions. Its usefulness is limited by its inability to obtain biopsy specimens, but it can direct the type and approach of subsequent enteroscopy by providing information on localization and extent of the detected lesions.