A nationwide epidemiologic survey of atopic diseases including allergic pollinosis was conducted in 9656 Japanese otorhinolaryngologists and their family members during the Japanese cedar pollen dispersion season in 2008 using methods identical to a previous survey that was performed in 1998. The survey response rate was 37.7% (compared with 42.8% in 1998). The overall prevalence rate of Japanese cedar pollinosis was 26.5%, which is an increase of approximately 9% from that noted in 1998. Similar increases were observed in all age groups, and the prevalence rate was similar between male and female respondents. A unimodal distribution was observed in male and female subjects, with a peak in both men and women aged in their 40s. Nationwide, a consistent positive relation was observed between the prevalence of Japanese cedar pollinosis and the regional Japanese cedar pollen counts. The prevalence rate of pollinosis other than Japanese cedar pollinosis and of perennial allergic rhinitis was 15.4% and 23.3%, respectively; both disease entities tended to occur more frequently in male than in female subjects. The prevalence rate of asthma, atopic dermatitis, and food allergy was 5.2%, 14.1%, and 3.9%, respectively. Our results suggest that the prevalence rates of atopic diseases including Japanese cedar pollinosis are dramatically increasing across all age groups in Japan. In particular, the increasing prevalence rate of Japanese cedar pollinosis seems to reflect higher exposure to the Japanese cedar pollen antigen in many prefectures.