Lung function is one of the strongest determinants of cardiopulmonary health and longevity. Long-term exposure to air pollution has been associated with decreased lung function. We undertook a retrospective study to compare the long-term consequences of air pollution in two areas of Japan: Mizushima, Okayama Prefecture and Kitakyushu, Fukuoka Prefecture. Industrialization began in Mizushima in the 1940s, whereas it began in Kitakyushu in the early 1900s. In Kitakyushu, levels of nitrogen dioxide have been higher compared to the Mizushima area. The subjects comprised 623 officially acknowledged victims of pollution-related illness (489 from Mizushima and 134 from Kitakyushu). All subjects were lifetime non-smokers and aged 65 years or older at the time of their last medical examination in 2009. Demographic data including diagnosed lung diseases and lung function at the time of certification assessment performed between 1973 and 1988 were obtained. The subjects from Kitakyushu were significantly younger (47.1 vs. 51.0 years, p < 0.001) and a higher percentage had asthma (91.2 vs. 36.8%, p < 0.001) compared to those from Mizushima. Furthermore, all measures of lung function were significantly lower in Kitakyushu group at the time of the certification assessment (p < 0.001) and at the follow-up (p < 0.001). However, no significant differences were observed in the annual mean decline in lung function between the two groups, despite the overall decrease in air pollution. In conclusion, the normal lung function is not restored even after improvement of air pollution. It is essential for every city to prevent air pollution.