In our report we describe concept, strategies and implementation of a central biosample and data management (CSDM) system in the three-centre clinical study of the Transregional Collaborative Research Centre "Inflammatory Cardiomyopathy - Molecular Pathogenesis and Therapy" SFB/TR 19, Germany. Following the requirements of high system resource availability, data security, privacy protection and quality assurance, a web-based CSDM was developed based on Java 2 Enterprise Edition using an Oracle database. An efficient and reliable sample documentation system using bar code labelling, a partitioning storage algorithm and an online documentation software was implemented. An online electronic case report form is used to acquire patient-related data. Strict rules for access to the online applications and secure connections are used to account for privacy protection and data security. Challenges for the implementation of the CSDM resided at project, technical and organisational level as well as at staff level.