The mucosal immune system is an integral part of the whole-body immune system, however its regulation, maturation and function are to a great degree independent. Mucosal lymphoid tissue is the largest immune organ of the body, that stands in the first line of defence against foreign invaders. The goal of the immune system is immunity, however immunologic unresponsiveness (tolerance) is a key feature of the mucosal immune system, because the organism must tolerate thousands of ingested and inhaled harmless food and bacterial antigens. The phenomenon of oral tolerance is the unique feature of the mucosal immune system. If abrogated, severe autoimmune diseases like Crohns disease, ulcerative colitis or coeliac sprue can develop. The quality of mucosal immune responses during newborn and infant age strongly influences the immune reactivity later in life. The most important factors influencing the development of mucosal immune reactivity are the feeding practices and microbial colonization. Manipulation of the mucosal immune system offers interesting possibilities to prevent infection as well as autoimmune diseases directly in the affected tissue, without participation of the whole-body immune system. In this review we present the most recent basic information about the mechanisms of mucosal immunity, ontogeny of mucosal immunity, mucosal tolerance and immunisation and the role of mucosal immunity in an inherited disease in which the main battlefield is the lung mucosa - cystic fibrosis.