We have analyzed peripheral blood stem cell (PBSC) mobilization, harvesting and selection properties in 128 patients with severe autoimmune diseases undergoing non-myeloablative autologous hematopoietic stem cell transplantation (HSCT) (50 patients with systemic lupus erythematosus (SLE), 43 - with multiple sclerosis (MS), 15 - with Crohn’s disease (CD), 8 - with scleroderma (Scl), and 12 - with others). Female/male ratio and mean age (range) were 90/38 patients, and 34 (14 to 59) years old, respectively. Mobilization regimen included cyclophosphamide 2g/m2 and G-CSF 10 mcg/kg (except for SLE patients 5 mcg/kg). Forty one patients underwent stem cell collection using Baxter CS300, 78 patients - Spectra, and for 9 patients both apheresis machines were utilized. The mean number of aphereses was 1.8 (range 1–10). Patients with SLE required the largest number of apheresis sessions (mean 2.4), comparing to patients with CD (mean 1.9), Scl (mean 1.4), MS (mean 1.3). Five patients additionally required bone marrow harvest for collection of adequate numbers of stem cells. One patient failed to reach CD34+ cell number of 1.0x106/kg, therefore did not proceed to HSCT. The mean number of CD34+ cells in each apheresis unit was 6.07+−6.96x106/kg (the highest of 9.22+−8.52x106/kg in patients with MS, and the lowest of 3.93+−4.48x106/kg in patients with SLE). Ninety eight patients underwent stem cell selection with CEPRATE SC (N=18), Isolex 300iv1.12 (N=2) or Isolex 300iv2.5 (N=78) stem cell concentrator. The mean purity of selected products was 74.3% (the highest of 81.1% attained in patients with Scl); mean recovery of CD34+cells was 61.2%. T cell reduction by average of 3.7 logs was achieved. The mean number of infused CD34+ cells was 7.24+−5.5x106/kg. The highest mean number of CD34+ cells/kg were infused to patients with MS (9.04+−6.74x106/kg), the lowest - to patients with SLE (5.78+−4.13x106/kg). We found a moderate positive correlation between peripheral blood (PB) CD34+ cells/ul and PB WBC/ul (R=0.34, p<0.05), PB platelets/ul (R=0.51, p<0.05) and a strong positive correlation between PB CD34+ cells/ul and the number of CD34+ cells/kg/apheresis (R=0.67, p<0.05). A weak positive correlation was observed between the number of infused CD34+cells/kg and faster WBC engraftment (ANC>500) and platelet engraftment (platelet count>20K). There was no toxicity observed in our patient population during peri-mobilization period except for 1 patient with SLE who died of disseminated mucormycosis 1 week after stem cell collection. Mobilization and selection of PBSC are safe and efficient in patients with severe autoimmune diseases undergoing non-myeloablative autologous HSCT.