Fruits are good sources of vitamins, minerals, fiber, and phytochemicals, which are known to reduce serum lipids, oxidative damage, and blood pressure as well as improve blood glucose control. The purpose of this study was to estimate nutrient quality indices of fruits by carrying out a critical analysis of pre-existing methods according to their nutritional compositions. Four methods were used to assess the nutrient indices of 26 fruits, which are frequently consumed by Koreans based on the fourth Korean National Health and Nutrition Examination Survey (2009). Naturally nutrient rich score (NNR), nutrient rich food (NRF), nutrient adequacy score (NAS), and nutrient density score (NDS) were used to calculate nutrient quality indices. The Korean Nutrition Society Food Composition database of fruits based on 100 g edible portions was used. The algorithm of each method included the mean percentage of daily values (Dietary Reference Intakes for Koreans, 2010) for particular nutrients based on consumption of 1,900 kcal/day. The relative score indicated that strawberries, kumquat, and lemon had high nutrient quality indices. In addition, mango, lemon, persimmon, strawberry, apricot, and tangerine fruits are rich in antioxidant nutrients such as ${eta}$-carotene, vitamin C, vitamin E, and selenium. However, scores of nutrient quality indices did not imply that higher scores of particular fruits are superior. We suggest moderate seasonable consumption a variety of fruits. Our results can be used as a reference for consumers when they choose fruits.