The Japanese diet is high in soy products and fish. A case–control study was conducted in Japan to investigate the relationship between dietary intake of isoflavones and fatty acids and lung function, breathlessness and chronic obstructive pulmonary disease (COPD). A total of 278 referred patients aged 50–75 years with COPD diagnosed within the past 4 years, and 340 community-based controls were assessed for respiratory symptoms and undertook spirometric measurements of lung function. A validated food frequency questionnaire was administered face-to-face to obtain information on habitual food consumption. Dietary intakes of isoflavones and fatty acids were derived from the Japanese food composition tables. The COPD patients had significantly lower habitual intakes of isoflavones (genistein and daidzein) and polyunsaturated fatty acids (PUFA; both omega-3 and omega-6) than control subjects. Lung function measures were found to be positively associated with isoflavones and PUFA intake. Substantial reductions in prevalence of COPD and breathlessness were observed for isoflavones, the respective adjusted odds ratio being 0.36 (95% confidence interval 0.19–0.68) and 0.60 (95% confidence interval 0.33–1.10) for the highest versus lowest levels of total isoflavone intake. The corresponding tests for linear trend were significant. High intakes of PUFA and omega-6 fatty acids (derived from foods excluding oils and fats as seasonings) also appeared to reduce the risks of COPD and breathlessness symptom, but no evidence of association was found for other types of fatty acids. The study provided evidence of possible protective effect of traditional Japanese diet against tobacco carcinogens.