Although fish and meat may exert opposing influences on chronic disease, information on the balance of intake between fish and meat to overall diet quality is limited, particularly in Japanese, who have a much higher fish intake than Western populations. The objective of this cross-sectional study was to test the hypothesis that intake balance between fish and meat is associated with food and nutrient intakes in young Japanese women. The subjects were 3716 Japanese dietetic students aged 18 to 20 years. Diet was assessed by a validated, self-administered diet history questionnaire. The dietary ratio of fish to meat was calculated from fish and meat intakes as a temporal indicator of overall intake balance. The ratio of fish to meat intake was associated positively with intakes of vegetables, fruits, pulses, dairy products, and alcohol, and negatively with those of energy-containing beverages and fat and oils. At the nutrient level, the ratio of fish to meat intake was associated negatively with intakes of energy, total fat, saturated fatty acids, n-6 polyunsaturated fatty acids, vitamin B(1), and zinc, and positively with those of protein, n-3 polyunsaturated fatty acids, dietary fiber, and key vitamins and minerals. After limiting analysis to nutrients derived from foods other than fish and meat, the ratio of fish to meat intake was positively associated with intakes of almost all vitamins and minerals examined. In conclusion, women who consumed more fish than meat (ratio >1) tended to choose more favorable food groups that included higher amounts of vegetables and fruits, resulting in a better profile of nutrient intake patterns.