The objective of this study was to evaluate the validity and reproducibility of a self-administered food frequency questionnaire (FFQ) to estimate nutrient and food intake in the subjects of the Japan Public Health Center-based prospective Study on Cancer and Cardiovascular Diseases (JPHC Study Cohort II). The FFQ was originally developed to estimate intake in the JPHC Study Cohort I. A total of 392 subjects were recruited from the entire cohort participants in the 6 areas of Cohort II on a voluntary basis. The subjects completed the FFQ used for the 5-year follow-up survey twice at approximately a 1-year interval. Seven-day dietary records (DR) and blood samples were collected 4 times at 3-month intervals over a year. Daily nutrient and food intakes from FFQ and DR were estimated. The Spearman correlation coefficients for estimated intakes were calculated between FFQ and DR for validity, and between 2 identical FFQs for reproducibility. Correlation coefficients for the validity ranged from 0.09 to 0.82 among various nutrients and food groups. The correlation coefficients for most of the nutrients and food groups were improved to a level comparable to that of Cohort I by energy-adjustment. Correlation coefficients for reproducibility ranged from 0.42 to 0.82, similar to those of Cohort I.