The gastrointestinal system is classically known for its function in digesting food for nutrient uptake, but it plays a much larger role in the general health of organisms. Understanding the relationships between the gastrointestinal tract and inflammation, the nervous system, diseases caused through disregulation of molecular components as well as its association with beneficial and pathogenic microbes have been the focus of intense research over the many decades. In this Special Issue we delve into histological, molecular, and evolutionary aspects of gastrointestinal system components in healthy and diseased tissues, to give a broad perspective on the different organs that make-up this system.