Kawasaki disease (KD) is an acute febrile systemic vasculitis and has been reported to be associated with allergic disease. The risk of atopic dermatitis (AD) in preschool children with KD has not been investigated. The study was to determine the longitudinal risk of the development of AD in preschool children with KD. A nationwide 5-year population-based study was performed using data from the National Health Insurance Database in Taiwan between 1999 and 2003. The risk factors for AD were compared between the 2 study groups during the follow-up period using the Cox proportional hazards model. In addition, plasma interleukin (IL)-5 levels were analyzed in normal subjects and KD patients. Among the 1440 subjects included, 21.6% developed AD during the 5-year follow-up period, of which 30.3% and 18.7% belonged to the study cohort and the comparison group, respectively. Children with KD were 1.25 times more likely to have AD than those in controls (P = 0.04). Levels of IL-5 and IgE were significantly higher in KD patients. Children with KD had a higher risk of developing AD during the 5-year follow-up period than the control group. Increased IL-5 and IgE levels may be key factors contributing to the risk of AD.