Almost all healthcare systems are currently facing fundamental challenges. New ways of organizing these systems based on novel knowledge and stakeholders’ different needs are required to meet these challenges at the appropriate time. In this context, the issue of biobanking has become a specific challenge having major implications for future research and policy strategies as well as for the healthcare systems in general. Medicine is currently undergoing remarkable developments from its morphological and phenotype orientation to a molecular and genotype orientation, promoting the importance of prognosis and prediction. Yet, the discussion about the relevance of integrating genome-based information into biobanks and about the role of genome-based biobanking for epidemiological research and public health is still at the beginning. The following article contributes to this discussion by focusing on the use of genome-based biobanking for epidemiological research, surveillance systems, health policy development, individual health information management and effective health services.