Current research projects using human biomarkers in their search for better knowledge on the interaction between environment and human health are facing sensitive ethical issues. Researchers may be put in situations in which it is unclear how to act in accordance with all necessary legal requirements on ethical aspects of research. As a consequence, scientific opportunities and important developments of which many individuals will benefit, may be missed. Sound scientific research in the field of environment and health may benefit from a "rethinking" of current theoretical frameworks and procedures issuing from clinical medicine, putting emphasis on decisional autonomy and the protection of the individual and to a much lesser degree taking into account the concept of "public interest". The protection of individuals participating in studies in the field of environmental health calls, e.g., new communication strategies from recruitment to debriefing, at individual as well as at societal levels. Research on the socio ethical aspects on HBM within ECNIS and Newgeneris is situated at the interface of science, ethics and law and should be considered in the context of one final goal: contributing to guidelines for a harmonized socio-ethical and legal approach of human biomonitoring activities in the EU, including procedures for effective and appropriate communication both a the individual and at the collective level, resulting in a European research atmosphere in which scientific research related to development and use of human biomarkers is promoted, and in which a simultaneous protection of the rights and dignity of the study subjects is guaranteed. A harmonized socio-ethical and legal approach not only increases the possibilities for comparison between data generated but may also allow for more equality in the protection of the rights of each citizen of the European Union.