The Helsinki Health Study cohort was set up to enable longitudinal studies on the social and work related determinants of health and well-being, making use of self-reported as well as objective register data. The target population is the staff of the City of Helsinki, Finland. Baseline data for the cohort were derived from questionnaire surveys conducted in 2000, 2001 and 2002 among employees reaching 40, 45, 50, 55 or 60 years of age in each year. The number of responders at baseline was 8960 (80% women, response rate 67%). Additional age-based health examination data were available. A follow up survey was conducted in 2007 yielding 7332 responders (response rate 83%). Measures of health include health behaviours, self-rated health, common mental disorders, functioning, pain, sleep problems, angina symptoms and major diseases. Social determinants include socio-demographics, socio-economic circumstances, working conditions, social support, and work-family interface. Further register linkages include sickness absence, hospital discharge, prescribed drugs, and retirement updated at the end of 2010. The cohort allows comparisons with the Whitehall II study, London, UK, and the Japanese Civil Servants Study from western Japan. The cohort data are available for collaborative research at Hjelt Institute, Department of Public Health, University of Helsinki, Finland.