Human biomonitoring (HBM) can be an effective tool to assess human exposure to environmental pollutants and potential health effects and is increasingly seen as an essential element in a strategy when integrating health and environment. HBM can be used (i) to prioritise actions and measures for policy making; (ii) to evaluate policy actions aimed at reducing exposure to potentially hazardous environmental stressors; and (iii) to promote more comprehensive health impact assessments of policy options. In support of the European Environment and Health Action Plan 2004-2010, European scientists, experts from authorities and other stakeholders joined forces to work towards developing a functional framework and standards for a coherent HBM in Europe. Within the European coordination action on human biomonitoring, 35 partners from 27 European countries in the COPHES consortium aggregated their experiences and expertise and developed harmonized approaches and recommendations for better comparability of HBM data in Europe via the elaboration of a harmonized study protocol. This protocol is the product of discussion and compromises on the selection of environmental exposures, national environmental health concerns, and political and health priorities. The harmonised approach includes sampling recruitment, and analytical procedures, communication strategies and biobanking initiatives. The protocols and the harmonised approach are a means to increase acceptance and policy support and to in the future to enable determination of time trends. The common pilot study protocol will shortly be tested, adapted and assessed in the framework of the DEMOCOPHES in 17 European countries, including 16 EU Member States. COPHES and DEMOCOPHES constitute important steps towards establishing human biomonitoring as a tool for EU environmental and health policy and to improve quantification of exposure of the general European population to existing and emerging pollutants.