We evaluated the relationships between children's housing, earthquake or tsunami damage affecting children, prevalence of allergic diseases, and levels of mite allergens and fungi on children's bedding after the Great East Japan Earthquake in four municipalities in Japan. We surveyed 464 children in Ishinomaki, 254 in Kami, 614 in Iwanuma, and 300 in Oiso whose parents or guardians had completed the International Study of Asthma and Allergies in Childhood questionnaire. We measured the levels of Dermatophagoides 1 allergens (Der 1) (Dermatophagoidespteronyssinus and Dermatophagoides farinae) on children's mattresses or futons and fungal counts (Aspergillus and yeast) between 2016 and 2018. Earthquake damage was significantly greater in Ishinomaki than in the other three municipalities. There were no differences in the prevalence of allergic disease among the four municipalities. Der 1 levels were significantly higher in Ishinomaki than in Iwanuma, but there were no differences among Oiso, Iwanuma, and Kami. Der 1 levels in children with asthma in Iwanuma and with allergic rhinitis in Kami were significantly higher than in those without these conditions. Total fungal counts and Aspergillus counts were highest in Kami and lowest in Oiso. Der 1 levels were significantly correlated with fungal counts in Kami and Iwanuma, but not in Ishinomaki or Oiso. Both Der 1 levels and total fungal counts in Ishinomaki were greater than those in other three municipalities. Housing and allergen-avoidance strategies varied among the four municipalities. Mite allergen and fungal levels in these Japanese municipalities might have been affected by the earthquake and tsunami, and these changes might have affected the prevalence of allergic diseases in children.