Although atopic dermatitis is known to be closely associated with food antigens, the actual changes in the gastrointestinal tract have not been clarified. The aim of this study was to investigate the macroscopic and histological features of the large intestine in patients with atopic dermatitis. We studied 15 outpatients who had generalized atopic dermatitis. Eight non-dermatitis subjects of a similar age without inflammatory bowel disease were also enrolled as controls. Total colonoscopy, pathological evaluation of biopsy specimens, and detection of Candida albicans were performed in all subjects. Four patients were re-examined after 6 months of treatment with an antifungal drug. Among the 15 patients with atopic dermatitis, 4 patients had melanosis coli. On pathological examinations, prominent infiltration of eosinophils and fragmentation of granulocyte nuclei were observed. There were no changes after an antifungal therapy. In the patients with melanosis coli, lipofuscin deposits were observed in the lamina propria. Candida albicans was not detected in any of the subjects. In conclusion, patients with atopic dermatitis may have a predisposition to develop chronic inflammation of the large intestine.