Colon has been shown to have a two-layered mucus system where the inner is devoid of bacteria. However, a complete overview of the mouse gastrointestinal mucus system is lacking. We now describe the mucus system from stomach to distal colon, including Peyer's patches, as mucus thickness, growth over time, adhesive properties and penetrability to fluorescent beads. Colon displayed spontaneous mucus release and all parts of the alimentary tract responded to carbachol and PGE₂ stimulation, except the distal colon and domes of Peyer's patches. Stomach and colon had an inner mucus layer that was adherent to the epithelium. In contrast, the small intestine and Peyer's patches had a single mucus layer that was easily aspirated. The inner mucus layer of the distal colon was not penetrable to beads the size of bacteria and the inner layer of the proximal colon was only partly penetrable. In contrast, the inner mucus layer of stomach was fully penetrable, as was the small intestinal mucus. This suggest a functional organization of the intestinal mucus system where the small intestine has loose and penetrable mucus that allow easy penetration of nutrients in contrast to the stomach where the mucus provides physical protection and the colon where the mucus separates bacteria from the epithelium. This knowledge of the mucus system and its organization improves our understanding of the gastrointestinal tract physiology.