An 18-year-old male high school student with school refusal and circadian rhythm disturbance is reported. At 17 years of age, he was unable to attend school because of a reversal of the daily rhythm and a moderate depressive feeling. Other circadian rhythms, including deep body temperature (DBT), and plasma melatonin, cortisol and beta-endorphin, also showed quite different or abnormal curves compared with those in normal controls. He was treated with methyl B12 and melatonin, which normalized the circadian rhythm, i.e. it became entrained to a 24-h period, and the DBT and hormonal rhythms became closer to normal patterns. These results suggest that desynchronization of the biorhythms, particularly the circadian rhythm, may be one of the important causes of school refusal in Japan, and melatonin and methyl B12 might be useful for treatment of the condition.