Maternal prepregnancy body mass index (BMI) may influence allergic diseases in the children who are the product of those pregnancies. The purpose of our study was to investigate the association between mothers' prepregnancy BMI and the risk of physician-diagnosed asthma, food allergy (FA), and atopic dermatitis (AD) in their children during the first 3 years of life. Data on mothers' prepregnancy BMI and physician-diagnosed asthma, FA, and AD in their children until the age of 3 years were obtained from the Japan Environment and Children's Study, a nationwide birth cohort study that has recruited 103,099 pregnant women between 2011 and 2014. Logistic regression analysis was used to analyze the results. We analyzed 67,204 mother-child pairs with available information on physician-diagnosed allergic diseases. The risk of asthma was significantly higher in children born to overweight mothers (adjusted OR [aOR] =1.17 [95% CI = 1.07-1.28]) and obese mothers (aOR = 1.28 [95% CI = 1.08-1.50]), whereas the risk of FA, cow's milk allergy, and egg allergy decreased significantly in children born to overweight mothers (aOR = 0.84 [95% CI = 0.76-0.92]; aOR = 0.78 [95% CI = 0.64-0.93]; and aOR = 0.83 [95% CI = 0.74-0.94]) and obese mothers (aOR = 0.81 [95% CI = 0.67-0.97]; aOR = 0.58 [95% CI = 0.36-0.87]; and aOR = 0.73 [95% CI = 0.56-0.93]) compared with in children born to normal weight mothers, respectively. Associations between AD and maternal BMI were not detected. Our study showed that an increase in mothers' prepregnancy BMI was associated with an increase in asthma prevalence and a decrease in FA prevalence in their children. Further studies are needed to reveal the mechanisms associated with maternal BMI and pediatric allergic diseases.