National biobank infrastructures are now being implemented in several European countries. Individually, biobanks are invaluable as national research resources; collectively, they are the critical elements needed for the actualization of the pan-European biobank infrastructure. The national biobank infrastructures are confronted with a number of challenges of legal, ethical, political, societal, financial and educational nature which must be articulated and addressed in order to optimize the use of the biobanks in national and international research. The community of researchers involved with these biobanks has charted the most pressing issues experienced by the national biobanks in their nascent stages of development. Our findings reveal great commonalities in the nature of the challenges that the national hubs are facing. These challenges and the strategies developed to address them are described in this paper.