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Objective: To determine whether the source of autologous hematopoietic stem cells altered the clinical outcomes of patients undergoing high dose chemotherapy and autologous hematopoietic stem cell transplantation (AHSCT) for aggressive lymphoma and to study the problem of minimal residual disease (MRD). Methods: 14 lymphoma patients who had lymphoma with high risk factors, relapsed lymphoma or refractory lymphoma received autologous bone marrow transplantation (ABMT). 14 lymphoma patients who were similar to ABMT group received autologous peripheral blood stem cells transplantation (APBSCT). Regimen of CBV (cyclophos phamide 50～60 mg/kg/d×2 d, carmustine 15 mg/kg/d×1 d,etoposide 45～60 mg/kg/d×1 d) was received by all the patients as conditioning regimen in the transplant pretreatment followed by ABMT or APBSCT. Autologous peripheral blood stem cell (APBSC) was mobilized by CTX 2g～3g/m2/d×2 d iv and G-CSF 5 μg/kg/d for five to seven days. MRD was continually supervised by PCR in bone marrow before and after transplantation. Cellular immunocyte function, such as natural killer cell (NK), CD3, CD4, CD8 and sIL-2R was tested before and twenty days after transplantation. Results: In ABMT group, the median time for hematopoietic recovery of absolute neutrophilia counts ≥0.5×109/L and platelet counts ≥20×109/L was +18 days and +20 days respectively. In contrast, the APBSCT group was both at 12 days. Patients who have undergone ABMT all got complete remission (CR), while 81.8% patients in APBSCT group got CR. The 3-year disease free survival (DFS) in APBSCT and ABMT group was 75% and 72.7% respectively (P＞0.05). The mean days of immunity recovering in APBSCT was ±20 days. After transplantation, MRD in 11 patients were positive, in whom 6 patients died. Conclusion: Aggressive lymphoma patients’ hemapoiesis recovered more rapidly in APBSCT group than that in ABMT group, but 3-year DFS had no statistical difference. Patients positive for IgH/TCR-γ by molecular PCR analysis had poor DFS. Molecur monitoring of MRD using PCR techniques seems to represent a reliable prognostic indicator. Immunotherapy in the patients whose bone morrow was positive for MRD post-AHSCT may intensify remission and reduce relapse rates.