The gastrointestinal tract, like the urinary, respiratory, reproductive tracts and the surface of the eye, has large surface areas which are in contact with the exterior environment. The mucosal tissues in the gastrointestinal tract are exposed to large number of exogenous, water or food born microbiota. Therefore, they serve as access routes for different types of bacteria, parasites, viruses, enzymes and toxins. In order to protect the mucosal tissues against pathogens and aggressive enzymes, which are necessary in digestive processes, they are covered by a resident microbial flora and also by a viscoelastic adherent mucous gel layer. The mucus layer acts as the first line of defense against threats and also as a positive environment for beneficial endogenous microbiota adapted for symbiotic living. The quantity and quality of mucus layers varies throughout the gastrointestinal tube and is often changed and disrupted during the occurrence disease. A disturbed mucus layer in the intestine can result in changes in the whole organism, such as: impaired immunity, loss of weight and weak food conversion, which is important, especially in food animals. That is why several researchers have focused on these changes, both in humans and other animals, to find out methods and countermeasures, which will facilitate the best protection for the mucus layer in the intestine. In this review, we describe the composition and function of the mucus layer and mucins in the intestine.