Biobanking in Europe has made major steps towards harmonization and shared standards for the collection and processing of data and samples stored in biobanks. Still, biobanks and researchers face substantial legal difficulties in the field of data protection and sample management. Data protection law was harmonized almost 15 years ago while rights in samples fall under the competence of the Member States of the EU. Despite the Data Protection Directive the field of data protection shows a substantial degree of deviation as public health was excluded from the harmonization. Biobanks seem to have substantially fewer difficulties to cope with in terms of the legal requirements in the field of sample management. This paper discusses the legal framework, experiences of different biobanks in Europe and potential ways forward. It also highlights the need for a health economic analysis of the costs and benefits of privacy protection in Europe. At the moment, policymakers seem to build their decisions on an insufficient evidence base which underestimates the potential value of biobanks for European public health. Within the past few years little progress has been achieved with regards to the development of a unified legal framework in Europe, The diversity in the legal system is also reflected in the different approaches of ethics committees towards biobanking. To secure the responsible and effective use of data and samples, more efforts are needed to come up with pathways for a solution.