Mortality in the Goto archipelago region of the Nagasaki prefecture in Japan is higher than the Japanese average. In this study, we investigated dietary intake, habitual physical activities, systolic and diastolic blood pressure, serum total cholesterol and high-density lipoprotein cholesterol of middle-aged women in the Narao community in the Goto archipelago. We compared these parameters with a Japanese sample, and analyzed the results according to body mass index (BMI) and age. The mean BMI of Narao women was higher than that of the Japanese sample. Serum cholesterol and blood pressure of Narao women correlated with BMI. However, dietary intake and physical activities did not differ between normal- and over-weight Narao women. The higher serum total cholesterol and diastolic blood pressure of Narao women, relative to the Japanese sample, could be explained by the presence of over-weight women in the Narao community. However, dietary and behavioral factors associated with higher BMIs could not be clarified in this cross-sectional study.