Background: In recent years, different clinical regimens of blood stem cell transplantation have been evaluated using peripheral blood stem cells (PBSC). Several types of cell separators were introduced for an efficient collection of PBSC. Material and Methods: In a prospective study at the Institute of Transfusion Medicine at the Münster University Hospital, two different cell separators were compared (COBE Spectra apheresis system, software version 5.1 / Fresenius AS.TEC 205 cell separator, software version 2.0.0) with regard to the collection of autologous peripheral blood stem cells. Patients: 7 patients (1 female, 6 male) with acute myeloid leukaemia (n = 2), multiple myeloma (n = 2), non-Hodgkin’s lymphoma (n = 2), testicular tumour (n = 1). Parameters of the investigation: efficiency of stem cell collection (yield/time), reduction of platelet counts and haemoglobin values during the apheresis process, product volume and ACD consumption. Results: The different parameters were evaluated at the basis of an equivalent length of time of each of the apheresis procedures. The volume of blood processed per time unit was significantly higher in the case of using the COBE Spectra apheresis system, and so was the ACD consumption. Upon comparison of yields of PBSC (CD34+ cells/kg body weight), we observed a trend in favour of a higher efficiency in the case of the COBE Spectra apheresis system. However, this trend did not reach statistical significance. The product volume was significantly lower in case of collecting PBSC with the Fresenius cell separator system than in case of using the COBE Spectra cell separator system. Carrying out the apheresis with the Fresenius cell separator system resulted in a diminished reduction of platelet counts and haemoglobin values in the course of the apheresis procedure, when compared to the COBE Spectra system. Conclusion: Both cell separators are well suitable for an efficient PBSC collection. Differences in the blood volume processed per time unit, the consumption of ACD, the yield of PBSC per time unit and the reduction of platelet counts and haemoglobin values allow for the individual selection of the optimal apheresis system guided by the clinical condition of each patient.