The combination of the local disinfection therapy against Staphylococcus aureus with the conventional therapy for atopic dermatitis has been widely used, and the improvement in skin lesions has been reported to be associated with a remarkable decrease in IgE levels and reagin antibody titers. We have already reported that affected organs were not only the skin but also the gastrointestinal tract in a case with atopic dermatitis. In the present study, the duodenal tissues were examined by biopsy in 32 patients with atopic dermatitis, and mild or chronic duodenitis was observed in all samples. Toxins were examined by PCR from 180 Staphylococcus aureus strains obtained from our patients. The detection rate of toxins was 82.8%. In many patients, antitoxin IgE antibody titers corresponding to their types of toxin and IgE levels were decreased in a parallel manner as time passed. We found 1 patient who complained of paresthesia in all four limbs, and her neurological and radiological examinations showed moderate cervical spondylosis. Neurological examinations revealed some abnormalities in 43 out of 50 patients with atopic dermatitis, such as hyperreflexia of the legs. Cervical MRI was carried out randomly and showed abnormal findings in 21 of 25 patients, in whom 18 duodenal tissues were examined by biopsies.