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Celiac disease has a morbidity of 0.2 to 1% in Europe and the United States (US), but appears to be extremely rare in Japan with only a few case reports. This report details a Japanese woman with celiac disease diagnosed by histopathological findings and the improvement of her clinical symptoms on a gluten-free diet. The woman was in her 60s and presented with diarrhea, abdominal pain, and vomiting which were repeatedly exacerbated over several weeks. Therefore, she was referred to our hospital for a detailed examination and treatment. Upper gastrointestinal endoscopy revealed a crude granular mucosa with an erythematous color in the duodenum. No special findings were noted on colonoscopy or capsular endoscopy. Histopathological findings of the duodenum noted villous atrophy, crypt hyperplasia, and lymphocytic infiltration within the surface epithelium, which were suspicious for celiac disease. A gluten-free diet was started which resulted in improved clinical symptoms. Repeat endoscopic imaging and histopathological findings after initiation of the gluten-free diet demonstrated improved small bowel villous atrophy. In this case, appropriate testing had ruled out inflammatory bowel disease, amyloidosis, infectious enteritis, parasitic disease, and allergies. Although anti-gliadin antibody (AGA) and anti-tissue transglutaminase antibody (ATTGA) were serologically negative, and HLA typing was HLA-DQ6, the patient was ultimately diagnosed as having celiac disease based on the characteristic pathological findings and clinical course. In many cases of celiac disease reported in Japan, serum antibodies such as AGA and ATTGA have not been detected, and HLA testing has been negative for DQ2 or DQ8. Therefore, it is possible that celiac disease in Japan might have different genetic and immunological characteristics than the disease in the US and Europe. In the future, additional cases with histology and molecular biological analysis are necessary to test this hypothesis.