To study the prevalence of atopic dermatitis, allergic rhinitis, and asthma in Taiwan, we analysed the claims data of a nationally representative cohort of 997,729 enrolees from the National Health Insurance register from 2000 to 2007. Overall, 66,446 patients were diagnosed with atopic dermatitis, and 49.8% of them had concomitant allergic rhinitis and/or asthma. The overall 8-year prevalences of atopic dermatitis, allergic rhinitis, and asthma were 6.7%, 26.3% and 11.9%, respectively. Children and adolescents had significantly higher prevalences of these atopic diseases. The prevalence of atopic dermatitis in females was lower than that in males before the age of 8 years, but became higher after that. Patients with atopic dermatitis were more likely to have allergic rhinitis and asthma. Those having both atopic dermatitis and allergic rhinitis possessed an even higher risk for asthma (odds ratio 9.04). The numbers of visits for atopic dermatitis were highest in late spring to mid-summer. These data suggest that atopic diseases are common in Taiwan.