Background: The Great East Japan Earthquake inflicted severe damage on the Pacific coastal areas of northeast Japan. Although possible health impacts on aged or handicapped populations have been highlighted, little is known about how the serious disaster affected preschool children's health. We conducted a nationwide nursery school survey to investigate preschool children's physical development and health status throughout the disaster. Methods: The survey was conducted from September to December 2012. We mailed three kinds of questionnaires to nursery schools in all 47 prefectures in Japan. Questionnaire "A" addressed nursery school information, and questionnaires "B1" and "B2" addressed individuals' data. Our targets were children who were born from April 2, 2004, to April 1, 2005 (those who did not experience the disaster during their preschool days) and children who were born from April 2, 2006, to April 1, 2007 (those who experienced the disaster during their preschool days). The questionnaire inquired about disaster experiences, anthropometric measurements, and presence of diseases. Results: In total, 3624 nursery schools from all 47 prefectures participated in the survey. We established two nationwide retrospective cohorts of preschool children; 53 747 children who were born from April 2, 2004, to April 1, 2005, and 69 004 children who were born from April 2, 2006, to April 1, 2007. Among the latter cohort, 1003 were reported to have specific personal experiences with the disaster. Conclusions: With the large dataset, we expect to yield comprehensive study results about preschool children's physical development and health status throughout the disaster.