Abstract Aim: To report on two children with encephalopathy caused by dietary thiamine deficiency due to newly developing nutritional problems in contemporary Japan. Subjects: A 1-year-old boy who had consumed 1 l of isotonic drinks per day for 4 months after an episode of diarrhea, and presented with ocular movement disorder, dystonia, and unconsciousness. The other subject was an 11-month-old boy who suffered from vomiting and somnolence; he and his mother had atopic dermatitis, and he had been on a low-allergen diet that strictly restricted intake of eggs, dairy products, meat, and fish since his early infancy. Results: Both patients showed decreased blood thiamine levels and magnetic resonance imaging revealed striatal and thalamic lesions. Thiamine administration yielded prompt improvement of symptoms, but cavitiform lesions in the bilateral putamen persisted in the first patient, accompanied by residual generalized dystonia. Marked elevation of blood/cerebrospinal lactate levels and severe hyponatremia were present in this patient. Conclusion: Thiamine-deficient encephalopathy in Japanese children due to excessive intake of sports drink or overstrict diet therapy for atopic dermatitis has been increasingly reported during the last decade, but is still not broadly recognized. These children may visit hospitals due to persistent vomiting as a symptom of thiamine deficiency, but glucose infusion without thiamine supplementation can aggravate their condition. Knowledge of these facts in medical and public settings is necessary to correct the erroneous impression that nutritional options given to ill children are necessarily beneficial for health, and promote awareness that they can be harmful when consumed in excess.