We introduce the national research biobanking infrastructure, BBMRI_CZ. The infrastructure has been founded by the Ministry of Education and became a partner of the European biobanking infrastructure BBMRI.eu. It is designed as a network of individual biobanks where each biobank stores samples obtained from associated healthcare providers. The biobanks comprise long term storage (various types of tissues classified by diagnosis, serum at surgery, genomic DNA and RNA) and short term storage (longitudinally sampled patient sera). We discuss the operation workflow of the infrastructure that needs to be the distributed system: transfer of the samples to the biobank needs to be accompanied by extraction of data from the hospital information systems and this data must be stored in a central index serving mainly for sample lookup. Since BBMRI_CZ is designed solely for research purposes, the data is anonymised prior to their integration into the central BBMRI_CZ index. The index is then available for registered researchers to seek for samples of interest and to request the samples from biobank managers. The paper provides an overview of the structure of data stored in the index. We also discuss monitoring system for the biobanks, incorporated to ensure quality of the stored samples.