Dietary intake modification is important for the treatment of chronic kidney disease (CKD); however, little is known about the association between dietary intake of antioxidant vitamins and kidney function based on gender difference. We examined the relationship of dietary intake of antioxidant vitamins with decreased kidney function according to gender in Japanese subjects. This population-based, cross-sectional study included 936 Japanese participants with the age of 40 years or older. A validated brief self-administered diet history questionnaire was used to measure dietary intakes of vitamin E and its four isoforms, vitamin A and vitamin C. Decreased kidney function was defined as estimated glomerular filtration rate <60 ml/min/1·73 m2. A total of 498 (53·2 %) of the study participants were women. Mean age was 62·4 ± 11·3 years. Overall, 157 subjects met the criteria of decreased kidney function. In the fully adjusted model, a high vitamin E intake is inversely associated with decreased kidney function in women (odds ratio, 0·886; 95 % confidence interval, 0·786–0·998), whereas vitamin E intake was not associated with decreased kidney function (odds ratio, 0·931; 95 % confidence interval, 0·811–1·069) in men. No significant association between dietary intake of vitamins A and C and decreased kidney function was observed in women and men. Higher dietary intake of vitamin E was inversely associated with decreased kidney function in middle-aged and older women, and the result may provide insight into the more tailored dietary approaches to prevent CKD.