One of the most common primary immunodeficiencies is the selective deficiency of IgA, which is present in very variable clinical conditions. This situation had conducted to different criteria with respect to the clinical meaning in a particular patient. The association of immunodeficiency of IgA and intestinal malabsorption is reported as statistically significant in the international literature. Nevertheless, the precise pathogenic connection between them is unknown. The relationship between bowel and immune system is reviewed here, and illustrated with the clinical case of a six-year old girl who presented with malabsorption and selective deficiency of IgA.