We report our clinical experience in autologous peripheral blood stem cells harvesting. A total of 40 patients with 112 apheresis procedures were analyzed, 88 with Cobe system and 24 with MCS3P system. Our results revealed that there was no significant difference in efficiency of CD34(+) cell harvesting between both apheresis systems, but the Cobe system had more nucleated cells collected and less red cell contaminated in the final PBSCs collections. The percentage of CD34(+) cells collected decreased significantly following the first day's harvesting (p = 0.026). There was a good correlation between the percentage of CD34(+) cells in PBSCs and colony forming units-granulocyte macrophage (CFU-GM) or burst forming unit-erythrocyte (BFU-E)(r = 0.909, p < 0.0001; r = 0.788, p < 0.0001, respectively). However, it was negatively correlated with the patient's age. The CD34(+) cells collected in patients with acute leukemias were also higher than those patients with other solid tumors. Ten cases (13%) with 15 apheresis procedures experienced side effects like numbness, nausea, fever, or headache etc. The Cobe system seemed to have higher frequency of side effects than that of MCS3P system (16% vs 4%). From our results, we concluded that both COBE and MCS3P system have similar efficiency and all patients could tolerate the apheresis procedures in peripheral blood stem cells harvesting. The CD34(+) cell can be used as a good parameter to estimate the amount of stem cells collected. The patient's age and disease pattern were significant factors influencing the CD34(+) stem cells collection in autologous peripheral blood stem cells harvesting.