Background: Differences in the effects of genetic factors on allergic diseases in two areas of the same race within the same country have not been studied with multiple logistic regression. Objective: To determine whether the effects of genetic factors on allergic diseases differ between two areas. Methods: A questionnaire provided information about family histories of allergic diseases and environmental factors was distributed to children attending kindergarten, elementary, or junior high school in two Japanese cities: Gifu, with a temperate climate, and Itoman, with a subtropical one. The number of subjects analyzed were 1,243 in Gifu and 1,953 in Itoman. Multiple logistic regression analysis was performed with SAS. Results: Multiple logistic regression analysis showed that in both cities children of families with allergic histories have significantly higher risk of contracting allergic disease and atopic dermatitis, even after being controlled for environmental factors. In Gifu, in families where both parents suffered from allergy, there was a higher incidence of allergic diseases than when only one of the parents was suffering from it. On the other hand, in Itoman there were no differences of relative risk between paternal history and maternal history. Conclusions: We speculated that there are some differences of genetic factors between different areas of the same country, and these differences of genetic effects may influence on the difference of the prevalence of allergic diseases as well as the environmental factors.