The Japan Multi-Institutional Collaborative Cohort (J-MICC) Study launched in 2005 by ten research groups throughout Japan aimed to examine gene-environment interactions in lifestyle-related diseases, especially cancers. This paper describes one component of the J-MICC Study, named Shizuoka Study, in which visitors aged 35 to 69 years to the Seirei Preventive Health Care Center in Hamamatsu were enrolled. Among 13,740 visitors matching eligibility criteria, 5,040 persons (36.7%) were enrolled from January 2006 to December 2007. Their lifestyle, disease history, and family history were surveyed using a self-administrated questionnaire. Blood and urine were collected from the participants. By the end of December 2008, 8 withdrawers and 1 ineligible participant had been removed, leaving 5,031 participants (3,419 males and 1,612 females) as the baseline dataset. Current smokers were 23.3% among males, and 4.4% among females, and those who drank once or more per month were 76.9% and 38.6%, respectively. Those with a cancer history were 3.0% for males and 3.8% for females. Measurements out of a normal range in males and females were 11.3% and 4.0% for diastolic blood pressure > or = 90 mmHg, 11.0% and 7.6% for systolic blood pressure > or = 140 mmHg, 5.9% and 1.7% for fasting blood glucose > or = 126 mg/dl, respectively. Collected information and specimens will be cooperatively used to examine the associations of biomarkers with lifestyle, genotypes, and their combinations, as well as for a part of the J-MICC Study.