Background: Capturing epidemiological signatures is essential to document burdens of disease and to design health care services, including prevention measures, clinical interventions, and policies. There are large geographical and ethnic variations in the epidemiology of allergic and immunological diseases. Various data are available from North America and Europe, but the epidemiology of allergic and immunological diseases in Asia is not well documented. Objective: To characterize epidemiological signatures of allergic and immunological disease in young children in Japan. Methods: This was a national, multicenter, prospective birth cohort study: Japan Environment and Children's Study (JECS). A general population of 103,060 women was enrolled during pregnancy. Allergic and immunological outcomes were assessed among young children using questionnaire data. Results: The prevalence of caregiver-reported immediate food allergy was 7.6%, 6.7%, and 4.9% at age 1, 2, and 3 years, respectively. Hen egg allergy was most common (5.4% prevalence at age 1 year) followed by allergies to cow milk and wheat. Several patterns of allergic symptom clusters were identified. Physician diagnosed, as reported by the caregiver, non-IgE mediated gastrointestinal food allergy affected 0.5% of infants. By contrast, caregiver-reported gastrointestinal food allergies affected 1.4% of children. Kawasaki disease affected 0.3% and 0.4% children, respectively, at age 1 and 3 years. Primary immunodeficiency disorders affected 0.005% children at age 3 years. Conclusion: These data provide important epidemiological signatures of allergy and immunology in young Japanese children including the age-specific prevalence of allergic disease, Kawasaki disease, and primary immune deficiency.