The data collection from cohort subjects at baseline is the core work for prospective study as well as follow-up. We set up 140, 420 cohort subjects (68, 722 men and 71, 698 women) (61, 595 in 1990 as Cohort I and 78, 825 in 1993 as Cohort II) based on resident registry of 29 districts under 11 Public Health Center areas and baseline survey were submitted for them. The survey consisted of the following three components: (1) self-administered questionnaire survey, (2) collection of blood samples (plasma and buffy coat) for deep-freezed storage and (3) collection of health check-up data. All survey were completed during the first five year of each study. Among all cohort subjects, 113, 461 (81%) (53, 375 men and 60, 086 women, 50, 245 in Cohort I and 63, 216 in Cohort II) returned the questionnaire and 49, 011 (35%) (18, 159 men and 30, 852 women, 24, 637 in Cohort I and 24, 374 in Cohort II) provide their blood. The health check-up data were collected from 47, 910 (34%) (17, 276 men and 30, 664 women, 23, 311 in Cohort I and 24, 599 in Cohort II). These data and blood samples serve as basis for the Japan Public Health Center-based prospective Study on cancer and cardiovascular diseases (JPHC Study). J Epidemiol, 2001; 11 (Suppl): S24-S29.