Objectives: To investigate trends in the prevalence of allergic disease over a 9-year period. Methods: Using National Health Insurance Service (NHIS) data, the annual number of patients with allergic disease was obtained for each regional subdivisions (small cities, counties, and districts) from 2003 to 2011. Annual populations for each sub-region were obtained and used to calculate the standardized prevalence. To compare prevalence within the study period, data was standardized spatially and temporally. For standardization, demographic data was used to obtain the registered population and demographic structure for 2010, which was used to perform direct standardization of previous years. In addition, a geographic information system (GIS) was used to visualize prevalence for individual sub-regions, and allergic diseases were categorized into five groups according to prevalence. Results: The nationwide outpatient prevalence of allergic rhinitis increased approximately 2.3-fold, from 1.27% in 2003 to 2.97% in 2013, while inpatient prevalence also increased approximately 2.4-fold,. The outpatient prevalence of asthma increased 1.2-fold, and inpatient prevalence increased 1.3-fold. The outpatient prevalence of atopic dermatitis decreased approximately 12%, and inpatient prevalence decreased 5%. Conclusions: There was a large difference between prevalence estimated from actual treatment data and prevalence based on patients’ self-reported data, particularly for allergic rhinitis. Prevalence must continually be calculated and trends should be analyzed for the efficient management of allergic diseases. To this end, prevalence studies using NHIS claims data may be useful.