Blood-derived autografts from patients with non-Hodgkin’s lymphoma (NHL) are frequently contaminated with clonogenic lymphoma cells. In order to obtain a more efficient lymphoma cell depletion from the transplants we compared the efficiency of different purging techniques: B-cell-directed depletion, CD34+ selection by immunomagnetic beads (IMB selection) or by immunoadsorption with a biotin-avidin column (BAC selection). Furthermore, two combination approaches were investigated: IMB selection after B-cell depletion as well as BAC selection after B-cell depletion. To assess purging efficiency, fluorescence-tagged (PKH26) K422 follicular NHL cells were admixed to the respective samples of leukapheresis products. BAC selection following B-cell depletion compared to BAC selection alone showed no significant differences in CD34+ purity (77 ± 12.5% vs. 70.7 ± 5.4%) (mean ± SE) or CD34+ recovery (35.3 ± 8.5% vs. 32.8 ± 10.4%), but a significantly (p < 0.005) higher lymphoma cell purging efficiency (log 4.32 ± 0.15 vs. log 2.92 ± 0.19). IMB selection following B-cell depletion and IMB selection alone resulted in a CD34+ purity of 40.8 ± 8.7% and 64.7 ± 7.9%, a CD34+ recovery of 47.2 ± 8.3% and 26.5 ± 6.5% and a lymphoma cell purging efficiency of log 3.68 ± 0.16 and log 3.48 ± 0.21, respectively. Lymphoma cell purging efficiency after either CD34 selection method alone as well as after either double purging method was significantly higher (p < 0.0005 and p < 0.00005, respectively) compared to B-cell depletion alone (log 1.44 ± 0.23). Our results argue for the combination of different purging modalities to achieve a maximal lymphoma cell depletion.