Floods are known to increase the level of allergens such as molds in the environments. Under climate change, the frequency of floods could be increased, which highlights the importance of understanding the impacts of floods on atopic diseases. However, there was a lack of studies. This study examines whether floods induce attacks of childhood atopic dermatitis (AD). A retrospective population-based study was conducted in Taiwan Island using Taiwan's National Health Insurance Research Database. Emergency room (ER) visits for AD were identified among children aged 0-12 years. Weekly data of flood occurrence, number of flood sites, temperature, and air pollution were obtained for each township of the identified cases. A time-stratified case-crossover design was used. The relationship between ER visits for AD and floods was assessed by conditional logistic regression, adjusting for weekly mean temperature, PM(2.5) and NO(2). There were a total of 55,488 ER visits due to AD during the study period. Such visits increased when flood occurred, and then declined. The effects of floods at the week of flood remained robust, with OR of 1.14 (95% CI = 1.01-1.28) for flood occurrence and 1.31 (95% CI = 1.10-1.55) for the number of flood sites, after adjusting for covariates. Such effects were slightly higher in boys and children aged 1-12 years. This study demonstrated the impact of floods on flare-up of childhood AD, and the effect was most prominently at the week of flood. Healthcare workers should be alarmed for potential increase of AD flare ups after flood events.