Quality assurance and safety of hematopoietic stem cells (HSC) with special emphasis on bacterial and fungal contamination is the prerequisite for any transplantation procedure. The aim was to determine the incidence rate of such contamination during processing of transplantation material with regard to HSC source: peripheral blood stem cell (PBSC), bone marrow (BM), or cord blood (CB). Analysis involved autologous and allogenic products dedicated for patients and comprised in all 4135 donations, including 112 BM (2.70%), 3787 PBSC (91.60%), and 236 CB (5.70%) processed in cell bank over the period 1996–2016. Aerobic and anaerobic contamination was determined.Analysis of the 20-year data revealed 42 contaminated products: 25 PBSC (0.66% of tested units) and 17 CB (7.20% of tested units). No microbial contamination of BM products was detected. Overall percentage of contaminated products was 1.01%, mostly with Staphylococcus epidermidis (61.36%). Bacterial contamination rate at cell bank is relatively low and processing in a closed system does not seem as crucial as might be expected. This is particularly true for BM components. Equally important are evaluation of donor’s medical status and condition of the puncture site for collection of source material. Implementation of appropriate sample collection procedures should help minimize the risk of false-positive results due to environmental contamination.