We examined the validity of food 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 a 19-food group measured by FFQ and DR were 0.42 (0.13-0.76) for men and 0.41 (0.02-0.75) for women. The median (range) for energy-adjusted correlation coefficients was 0.38 (0.08-0.76) for men and 0.32 (0.06-0.66) for women. The mean percentage of classification into the same categories between the two methods was 30% in men and 31% in women. Only 2% in men and 3% in women of subjects were classified into the extreme opposite categories. When we adjusted for area, the median correlation coefficients were decreased in crude intakes (0.34 in men and 0.28 in women), whereas no remarkable change was observed in energy-adjusted intakes (0.33 in men and 0.29 in women). 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 food groups examined. But intake levels both at population and individual levels were difficult to estimate.