Background: Most studies regarding the association of obesity with asthma have been performed in the Western countries. This study is a nationwide survey conducted in Japan. Methods: A cross-sectional and questionnaire-based survey was performed among children aged 6-7, 13-14, and 16-17 years, using the ISAAC questionnaire. Overweight was defined as BMI >= 90th according to the reference values for Japanese children obtained during 1978-1981. Results: Of a total of 179 218 children, 149 464 replied to the questionnaire (response rate 83.4%). After omitting incomplete data, 139 117 were analyzed. In all the age groups, being overweight was associated with current asthma after adjustment for confounding factors (adjusted OR: 1.24 in children 6-7 years of age, 1.31 in those 13-14 years, and 1.32 in those 16-17 years). These tendencies were observed in both genders. Overweight was a risk factor for nocturnal cough, independent of current asthma in the older age groups (adjusted OR: 1.21 in children 13-14 years, and 1.17 in those 16-17 years). Conclusions: There is a clear association between obesity and current asthma in Japanese school-aged children. Mechanisms through which obesity related with nocturnal cough might be different from those of obesity-associated asthma.