Background: Professional biobanks become increasingly important for fostering personalized medicine. While setting up and operating a high-quality collection of biomaterial specimens, biobank managers must face several challenges concerning quality management.

Objectives: Designing and implementing a data management, which ensures patient's privacy and simultaneously provides researchers with all relevant patient information, is particularly demanding. The requirements of all involved stakeholders must be considered without impairing the biobank's efficiency.

Methods: To link biomaterial samples to medical data documented in different contexts, an asymmetric encryption scheme with pseudonymization for existing clinical identifiers was implemented.

Results: The presented pseudonymization scheme allows establishing a comprehensive flow for pseudonymized data for biomaterial samples.

Conclusion: Most of the content stored in clinical databases, except for personally identifying data, can be evaluated, combined with individually documented medical data and associated this to a biomaterial sample without revealing personally identifying data.