The intestinal mucosa not only forms a physical barrier but also coordinates the innate and adaptive immune defence in the intestines to protect the body from potentially harmful substances and pathogens. The intestinal immune system is constantly active and ensures a regulated defence and tolerance. Diseases with impaired immune defences therefore often lead to infectious, chronic inflammatory or autoimmune intestinal diseases with a clinical picture of diarrhea, bloody stools and malabsorption as well as failure to thrive in children and weight loss in adolescence. Hence, immunodeficiencies should be considered when investigating chronic bowel disease. Recognizing an underlying immunodeficiency is crucial for choosing between treatment approaches, which is why genetic diagnostics should be carried out at an early stage. Depending on the underlying disorder of the immune system, there are typical clinical, immunological and histological features. Known gene variants can be associated with typical phenotypes but sometimes there is no genotype-phenotype correlation. More frequently, however, signs and symptoms, histological alterations and inflammatory markers are common to a number of monogenetic defects. Consequently, patients with a suspicion of immunodeficiency benefit from next generation sequencing (NGS).