Most of researches on the impact of indoor air pollutants on atopic dermatitis (AD) have been based upon animal models, in vitro experiments and case-control studies. However, human data to elucidate the role of indoor air pollution on worsening symptoms of pre-existing AD from a longitudinal study are scarce. The objective of this prospective study was to evaluate the effect of indoor air pollution on AD symptoms in children. We surveyed 30 children with AD in a day-care centre, which moved to a new building during the study. These children stayed there for 8 hours a day Monday through Friday, and their daily symptom scores were recorded. Indoor and outdoor air pollutant levels were continuously measured 24 hours a day for 12 months (Period 1 to 4). Data were analyzed using a generalized linear mixed model. Compared to the period before moving (Period 1), concentrations of indoor air pollutants mostly increased after moving (Period 2) and decreased by natural ventilation and bake-out (Periods 3 and 4). The rate of positive AD symptom increased from 32.8% (Period 1) up to 43.8% (Period 2) and 50.5% (Period 3), then decreased to 35.4% in Period 4 (P < 0.0001). When the delayed effects of indoor air pollutants on AD symptoms 2 days later were evaluated, AD symptoms significantly increased by 12.7% (95% CI: -0.01 to 27.1) as toluene levels increased by 1 ppb (P = 0.05). In conclusion, indoor air pollutants increase the risk of AD aggravation in children and toluene in the indoor environment might act as an aggravating factor.