We collected information concerning diagnosed allergy from 2027 school children in Japan, Taiwan and Vietnam. Children were classified according to the age and sex-specific body mass index (BMI) per-age as indicator of weight status. Logistic regression was performed to examine the relationship between percentiles of BMI-per-age and allergy. Compared with children at the lowest percentile group Taiwanese children at > 85th percentile group showed a tendency toward higher risk of allergy (OR = 1.79, 95% CI 0.98 to 3.27; p = 0.060). When children with rhino-conjunctivitis were excluded from the analysis the association reached statistical significance (OR = 2.89, 95% CI 1.08 to 7.75; p = 0.035). Vietnamese children at > 85th percentile group showed a significantly higher risk of allergy (OR = 2.34, 95% CI 1.06 to 5.17; p = 0.035). This association was not observed when children with atopic dermatitis or food allergy were excluded from the analysis, although a tendency toward increased risk of allergy at BMI-per-age > 85th percentile remained. Our study sample of Japanese school children showed no association between being overweight and allergy.