Understanding the structures and the function of the gastrointestinal tract (GI tract) in healthy individuals is important to understand malfunctions and diseases. It enables the explanation of difficult and complex interactions and modern therapeutic regimens. The GI tract consists of several organs, and the main tasks are digestion, decontamination of food and environmental elements, and, most importantly, immunity. In a complex interaction with innate and adaptive immunity and a lot of key factors like the microbiota, the intestinal immune system enables the human individuum to live in an often hostile environment. It makes it possible for an individuum to recognize and memorize protective or harmful agents and to start defensive mechanisms. Dysbalances lead to defects with malfunctions and diseases. In most diseases, the aetiology of these defects is not well understood. Underlying genetic causes and environmental triggers can lead to immunological and microbiota dysbalances.