This study aims to analyze the trends in the Japanese prevalence of asthma, allergic rhinitis, and atopic dermatitis by using age-period-cohort (APC) analysis. Data regarding the prevalence of diseases from 1999 to 2017 were collected from Patient Survey in Japan. The data were divided according to age groups ranging from 0-4 years old up to 65-69 years old in 5-year increments. A cohort was defined for each age group of each year with a one-year shift, and cohorts born from 1930-1934 up to 2013-2017 were examined. We used Bayesian APC analysis to decompose the changes in prevalence into age, period, and cohort effects. Results show that the period effect for asthma began to increase in 2008, and those of allergic rhinitis and atopic dermatitis began to increase in 1999. The cohort effects for asthma and atopic dermatitis increased rapidly in cohorts born from approximately 1950 to 1980 and then decreased thereafter. Furthermore, the cohort effect for allergic rhinitis increased from cohorts born in approximately the late 1970s for men and in 1990 for women. The time points with increasing cohort effects for asthma and atopic dermatitis are consistent with the history of air pollution accompanied by rapid economic growth in Japan. The onset of the increased cohort effect for allergic rhinitis was also relatively consistent with the time point at which the mass scattering of pollen began.