Background: An association of Crohn’s disease (CD) with food allergy has been discussed, but the role of food-specific IgE has not been clarified yet. Since CD is combined with immune complex formation, we examined in the present study whether anti-IgE autoantibodies in such complexes might hinder the determination of specific IgE. Methods: In order to elucidate the role of food-specific IgE in CD, we tested sera from CD patients (n = 107), healthy controls (n = 65) and allergics subjects (n = 7) for their IgE binding to food antigens (yeast, corn, celeriac, wheat) by an immunodot assay. After determining levels of IgE/IgG anti-IgE immune complexes, we purified them from serum pools of patients with CD, allergic subjects and healthy controls by affinity absorption using a monoclonal anti-IgE antibody. These purified immune complexes were treated by low pH (pH = 4) in order to dissolve them and to increase the detectability of food-specific IgE by RAST and CAP assay. Results: In CD sera no food-specific IgE could be detected, but levels of immune complexes of IgE and IgG anti-IgE autoantibodies were statistically significantly increased compared to healthy controls. pH treatment of purified IgE/IgG anti-IgE immune complexes resulted in a significant increase in specific IgE to yeast, corn, wheat and celeriac detected by RAST, however, only in the serum sample purified from allergic subjects. After pH treatment of CD immune complexes, specific IgE levels remained still very low. Conclusion: Thus, even if IgE seems to represent an autoantigen in CD, it is unlike to specifically participate in the pathophysiology of the putative food adverse reactions.