The prevalence of allergic diseases has been increasing in developing areas but has reached a plateau in many developed areas. Regular surveys are imperative to assess the disease burden for the prioritization of resource allocation. We examined the change in the prevalence of wheezing, allergic rhinitis (AR), and eczema in school-aged children with possible associative factors and possible health effects of school air quality. This was the third repeated cross-sectional study conducted in 2015-2016 using the International Study of Asthma and Allergies in Childhood (ISAAC) protocol. Our first and second surveys were conducted in 1994-1995 and 2000-2001, respectively. Regarding the third survey, we recruited 3698 children aged 6-7 from 33 local schools in 18 districts. Air quality, temperature, and humidity were also measured. The changes in prevalence, multiple regression, and GLIMMIX procedure were analyzed. From our first survey to our third survey, the increased prevalences for lifetime wheeze, current wheeze, lifetime rhinitis, current rhinitis, current rhinoconjunctivitis, lifetime chronic rash, and current chronic rash were 4.2%, 2.1%, 12.5%, 12.6%, 14.2%, 3.9%, and 4.1%, respectively. Increased prevalence of parental atopy had the strongest association with an increased prevalence of each of these seven health outcomes. There was no significant association between school air pollutant levels and the prevalence of health outcomes. There was an increase in the prevalence of wheezing, allergic rhinitis, and eczema across the surveys. The most important associated risk factor identified was the increased prevalence of a parental history of atopy.