The Ogasawara Islands, away from mainland Japan, belong to a subtropical area. Although the daily eating habits and food are relatively similar to that on the mainland, the living environment is quite different. The prevalence of allergic diseases in the Ogasawara Islands is unknown. This study aimed to identify the prevalence of allergic diseases in the Ogasawara Islands.A survey was conducted among all children belonging to preschool, elementary school, and junior high school in the Ogasawara Islands. A questionnaire was prepared in accordance with the International Study of Asthma and Allergies in Childhood (ISAAC) core written questionnaire in bronchial asthma (BA) and the West Japan Study of Asthma and Allergies in Childhood core written questionnaire for atopic dermatitis (AD), allergic rhinitis (AR), and food allergy (FA). At the same time, height, weight, duration of dwelling on the island, home environment, lifestyle, and exercise habits were also asked.The target population comprised 352 children, of whom 284 (80.6%) completed the questionnaires. The current prevalence was 9.3% for BA, 4.3% for AD, 17.8% for AR, and 3.0% for FA. Significantly lower rates of current BA and AD were observed compared to previous reports from Japan. The percentage of children belonging to sports clubs, and exercising more than 3 times per week at the Ogasawara Islands is higher compared with the national average.The lower prevalence of BA and AD in the Ogasawara Islands implies the influence of differences in the living environment and exercise habits.