We examined the validity of energy and 16 nutrient intake measurements from a self-administered food frequency questionnaire (FFQ) used in the 5-year follow-up survey of the JPHC study using 28- or 14-day dietary records (DR) as the gold standard. The median (range) correlation coefficients between 16 nutrients measured by FFQ and DR were 0.52 (0.31-0.81) for men and 0.41 (0.22-0.56) for women. The median (range) for energy-adjusted correlation coefficients was 0.40 (0.22-0.82) for men and 0.39 (0.15-0.48) for women. With further adjustment for area, it was 0.41 and 0.35, respectively. The mean percentage of classification into the same categories between the two methods was 33% in men and 30% in women. Only 2% of subjects were classified into the extreme opposite categories. In conclusion, the results suggest that the FFQ can be used in the JPHC Study Cohort I to rank individuals according to the intakes for most of the nutrients examined.