There have been many studies of the prevalence of atopic dermatitis (AD), but few population-based epidemiologic studies measure the prevalence in Japan among children aged 5 years and younger. We examined the prevalence of AD, serum total IgE levels and specific IgE antibodies to 10 common allergens among children in Ishigaki Island, Okinawa, Japan in 2001. We also obtained information on the predictability of the U.K. Working Party diagnostic questionnaire criteria for AD in this population. Five hundred and sixty five children aged 5 years and younger were enrolled in this study with informed consent from their parents. The questionnaire of the U.K. Working Party diagnostic criteria for AD was translated into Japanese, and the parents completed the questionnaire sheet. Physical examination and blood sampling were done for all children. Thirty-nine out of the 565 (6.9%) children were diagnosed with AD by physical examination. The total and specific IgE levels were significantly higher in the children with AD than in those without AD. High levels of total IgE were found in 33.3% of the children with AD. A specific IgE to one or more allergens was detected in 64.1% of children with AD. However, a substantial population of children without AD also had high levels of total IgE (12.7%) and a specific IgE to one or more allergens (30.2%), and the increment of total and specific IgE levels was significantly associated with age. The percentage of positive answers to the questionnaire of the U.K. Working Party diagnostic criteria for AD was significantly higher in children with AD (59.0%) than in children without AD (5.3%) (P<0.0001). Its specificity was 94.7%. The false negative rate was 41%. In conclusion, the prevalence of AD was relatively low in children in Ishigaki Island. High levels of total IgE were found in only one third of children with AD under 5 years of age. The Japanese translated form of the questionnaire of the U.K. Working Party diagnostic criteria for AD should be refined to improve its sensitivity.