Two kinds of food frequency questionnaire (FFQ)s were used in the baseline and 5-year follow-up survey of the Japan Public Health Center-based prospective Study on Cancer and Cardiovascular Diseases (JPHC Study Cohort I), a prospective follow-up study with 50,000 population. The former (FFQ00) was a 44-item FFQ without standard portions/units and the latter (FFQ05) was a 138-item FFQ with standard portions/units. To validate these FFQs, a 7-day dietary record (DR) survey with blood and urine collection was conducted in four seasons in the Ninohe (Iwate), Yokote (Akita) and Saku (Nagano) Public Health Center (PHC) areas, and in two seasons in the Ishikawa (Okinawa) PHC area. Another FFQ00 and FFQ05 have also been employed at a one-year interval to measure reproducibility. A total of 102 men and 113 women provided complete 28-day DRs (14 days for Okinawa) and then filled out both FFQs after three or six months. A total of 92 men and 104 women provided blood twice, and 37 men and 65 women provided 24-hour urine twice. The data from these surveys have been used to measure the validity and reproducibility of the estimated food groups and nutrient intake by each FFQ.