BACKGROUND: Customarily, bedrooms in Japan are left unheated. Although several studies have reported that the use of a heating system has positive outcomes on respiratory infection and asthma, the preventive effect of heating systems against infectious diseases in children is not well known. METHODS: We conducted a cohort study using two questionnaire surveys, one before the winter season in November, 2018 and the second after winter in March, 2019. Participants were 155 children who did not use a heating system in the bedroom and 156 children who did. RESULTS: Having a heated bedroom with a heating system was associated with decreased odds for the frequency of cold (≥3 times) (adjust odds ratio [AOR] 0.35; 95% confidence interval [CI], 0.19-0.65), duration of fever (≥3 days) (AOR 0.38; 95% CI, 0.22-0.66), duration of medicine for a cold (≥3 days) (AOR 0.91; 95% CI, 0.87-0.95), hospital visit due to cold (≥3 days) (AOR 0.54; 95% CI, 0.31-0.94), absence from school or nursery (≥3 days) (AOR 0.43; 95% CI, 0.27-0.70), influenza infection (AOR 0.43; 95% CI, 0.26-0.71), and gastroenteritis (AOR 0.39; 95% CI, 0.21-0.72). Influenza vaccination reduced the odds of influenza infection (AOR 0.36; 95% CI, 0.22-0.59) and absence from school or nursery (≥3 days) (AOR 0.62; 95% CI, 0.39-0.99). CONCLUSION: This study implies that the heating of bedrooms may have a preventive effect against infections among children. Broader dissemination of this knowledge in Japan will require cultural change through public health awareness.