BACKGROUND: The Japanese database of food composition was revised in 2020, during which both the number of food items and the number of food items measured for sugars, amino acids, and fatty acids were increased. We evaluated the validity of estimated intakes of sugars, amino acids and fatty acids using a long-food frequency questionnaire (FFQ) among middle-aged and elderly Japanese. METHODS: From 2012 to 2013, 240 men and women aged 40-74 years from five areas in the JPHC-NEXT protocol were asked to respond to the long-FFQ and provide a 12-day weighed food record (WFR) as reference. The long-FFQ, which included 172 food and beverage items and 11 seasonings, was compared with a 3-day WFR, completed during each distinct season, and validity was assessed using Spearman's correlation coefficients. RESULTS: Percentage differences based on the long-FFQ with the 12-day WFR in men and women varied from -83.9% to 419.6%, and from -75.8% to 623.1% for sugars, -17.5% to 2.8% and -5.8% to 19.6% for amino acids, and -58.5% to 78.8% and -43.4% to 129.3% for fatty acids, respectively. Median values of correlation coefficients for the long-FFQ in men and women were 0.52 and 0.42 for sugars, 0.38 and 0.37 for amino acids, and 0.42 and 0.42 for fatty acids, respectively. CONCLUSIONS: The long-FFQ provided reasonable validity in estimating the intakes of sugars, amino acids, and fatty acids in middle-aged and elderly Japanese. Although caution is warranted for some nutrients, these results may be used in future epidemiological studies.