The 25th anniversary symposium for the Fondation Jean Dausset–CEPH will be followed by a workshop on new technologies for analysis of genetic variation and molecular phenotypes in epidemiological-scale studies of human disease. The purpose of the workshop is to introduce researchers to new methodologies that underpin these studies, particularly in the context of on-going research funded by the EU. Progress in technological developments for DNA, RNA, protein and metabolite analysis, data handling and interpretation will be reviewed. Examples of the application of these technologies for epidemiological-scale studies in biobanks and different common complex diseases will be given.