ObjectiveTo investigate the relationship between personal experience of the Great East Japan Earthquake and various disease types among nursery school children.DesignWe conducted a nationwide survey of nursery school children born between 2 April 2006 and 1 April 2007. Nursery school teachers completed questionnaires if they agreed to join the study. Questionnaire items for children consisted of their birth year and month, sex, any history of moving into or out of the current nursery school, presence of diseases diagnosed by a physician at the age of 66–78 months and type of disaster experience. The survey was conducted from September 2012 to December 2012.SettingJapan, nationwide.ParticipantsA total of 60 270 nursery school children were included in the analysis, 840 of whom experienced the disaster on 11 March 2011.Main outcome measuresThe health status of children 1.5 years after the disaster based on nursery school records.ResultsExperiencing the disaster significantly affected the prevalence of overall and individual diseases. Furthermore, there was a difference in disease prevalence between boys and girls. In boys, experiencing the tsunami (OR 2.53, 95% CI 1.22 to 5.24) and living in an evacuation centre (OR 2.92, 95% CI 1.46 to 5.83) were remarkably associated with a higher prevalence of atopic dermatitis, but these trends were not observed among girls. Instead, the home being destroyed (OR 3.50, 95% CI 2.02 to 6.07) and moving house (OR 4.19, 95% CI 2.01 to 8.71) were positively associated with a higher prevalence of asthma among girls.ConclusionsOur study indicates that experiencing the disaster may have affected the health status of nursery school children at least up to 1.5 years after the disaster. Continuous monitoring of the health status of children is necessary to develop strategic plans for child health.