While Japanese diets have attracted considerable attention because of, for example, the long-life expectancy in Japan, their health benefits have not been examined. In the present study, we cross-sectionally examined whether adherence to the food-based Japanese dietary guidelines is associated with metabolic risk factors in 1083 Japanese women aged 18–22 years. Based on the Japanese Food Guide Spinning Top, adherence to the food-based Japanese dietary guidelines was assessed using dietary information on consumed servings of grain dishes, vegetable dishes, fish and meat dishes, milk and fruits and energy from snacks and alcoholic beverages during the preceding month, which was derived from a comprehensive diet history questionnaire. Higher dietary adherence was associated with higher intakes of protein, carbohydrate, dietary fibre, Na, K and vitamin C, and lower intakes of total and saturated fat. There was also an inverse association between dietary adherence and dietary energy density. After adjustment for potential confounding factors, dietary adherence was inversely associated with waist circumference (P for trend = 0·002). It also showed an inverse association with LDL-cholesterol concentrations (P for trend = 0·04). There was no association with the other metabolic risk factors examined, including BMI, systolic and diastolic blood pressure, total and HDL-cholesterol, TAG, glucose, glycated Hb and insulin concentrations. In conclusion, higher adherence to the food-based Japanese dietary guidelines, which was characterised by favourable dietary intakes of foods and nutrients as well as lower energy density, was associated with lower waist circumference and LDL-cholesterol concentrations in this group of young Japanese women.