Food incompatibilities affect approximately 20% of the general population in Western countries. In about one quarter of the affected children and one tenth of affected adults, the incompatibility is based on an allergy, that is, on an immunologically generated incompatibility reaction. Gastrointestinal symptoms occur in a third of these cases. Food allergies are caused by IgE-dependent orIgE-independent immunologic reactions, which lead to an inflammatory reaction, in which mast cells, eosinophilic granulocytes, and other cells are involved. Both genetic and environmental causes are under consideration. New findings concerning the interaction between the innate immune system and intestinal microflora have generated innovative therapeutic concepts, including the use of probiotics to prevent food allergies. The development of recombinant allergens and varieties of allergens will improve diagnostic possibilities and bring new therapeutic options, such as hyposensitization and induction of immunologic tolerance. Food intolerances (non-immunologic food incompatibilities often caused by specific enzyme deficiencies) must be diagnostically differentiated from food allergies.