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: The transfer of samples to the biobank needs to be accompanied by the extraction of data from the hospital information systems, and these data must be stored in a central index, which is used mainly for looking up samples. Since BBMRI_CZ is designed solely for research purposes, the data are anonymised prior to their integration into the central BBMRI_CZ index. The index can then be used by registered researchers to search 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 a monitoring system for the biobanks, which is incorporated to ensure the quality of the stored samples.