The gastrointestinal mucosa is remarkably well protected against infections in most patients with primary B-cell deficiency. Individual variations probably reflect differences in residual or compensatory secretory immunity as well as in the natural defense systems. Moreover, the intraepithelial lymphocytes seem to respond both in generalized defects and in selective IgA deficiency and may have protective potential. The clinical problems are related rather to the upper respiratory tract in which only little IgM is usually produced, even in IgA deficiency. Despite abundant intestinal production of IgM, however, immune exclusion is clearly suboptimal in the gut of IgA-deficient subjects; more than half of them have raised levels of serum IgG antibodies to cow milk proteins and other dietary antigens as well as circulating immune complexes containing such proteins. These phenomena, which indicate increased influx of antigens, may contribute to the relatively high incidence of autoimmune and allergic disorders seen in selective IgA deficiency, including celiac disease. In generalized B-cell deficiencies it is difficult to exclude celiac disease in some patients, and others have gastrointestinal lesions resembling inflammatory bowel disease.