This study was purposed to evaluate the long-term outcome and the safety of autologous peripheral blood mononuclear cells (PBMNC) treated by interleukin 2 (IL-2) and granulocyte-macrophage colony stimulating factor (GM-CSF) in the therapy of patients with aplastic anemia (AA). The therapy of 49 patients admitted BG in hospital from April 2001 to December 2007 were analyzed retrospectively. PBMNC were isolated and cultured for 48 hours in presence of IL-2 and GM-CSF. Cells were collected, and 6 × 10(6) - 1 × 10(8) PBMNC were intravenously injected weekly for 4 - 22 months. Hematopoietic recovery was evaluated by examinations of peripheral blood, bone marrow aspirates and bone marrow biopsy. Flow cytometry was used to assess the peripheral T cell subsets before and after treatment. Polymerase chain reaction was performed to observe the clonal diversity of T cell receptor variable β-chain (TCR-Vβ) recombination. The results showed that 37 cases were cured and none of them relapsed during the follow-up, 5 cases were in partial remission, 3 cases got improvement, and 4 cases showed no response. The total efficiency reached up to 91.8%. The ratios of CD4(+)/CD8(+) subsets were abnormal in 39 patients prior to the treatment, and 31 cases restored to the normal range after cell transfusions. Analysis on the clonal diversity of TCR-Vβ recombination in 11 patients showed the transition from monoclonal or biclonal spectratype to polyclonal one. No long-term side effects were documented. It is concluded that the treatment with PBMNC treated by IL-2 and GM-CSF is generally safe and effective. The underlying mechanisms may be in relation to the restoration of cell immunity.