Background: Differences in the prevalence of allergic diseases and the effects of genetic and environmental factors on these diseases in two areas of the same country have not been examined by multiple logistic regression. Objective: To determine whether the effects of genetic and environmental factors on allergic diseases differ between two areas. Methods: A questionnaire was distributed in March 1991 to children less than 16 years old 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 1243 in Gifu and 1953 in Itoman. Multiple logistic regression analysis was performed using SAS. Results: The prevalences of allergic diseases and atopic dermatitis in Gifu were significantly higher than in Itoman (P < .05). In contrast, the prevalence of bronchial asthma in Itoman was significantly higher than in Gifu (P < .05). Multiple logistic regression analysis showed that in both cities children of families with allergic histories have significantly higher risk of contracting an allergic disease and atopic dermatitis. The prevalences of allergic diseases and atopic dermatitis were higher in Gifu than in Itoman, even after being controlled for genetic and environmental factors. Conclusions: The increased risk of contracting an allergic disease and atopic dermatitis for the children in Gifu may be due to such factors not included in the study as climate, eating habits, or the level of air pollution.