The two clinical scale devices currently available for CD34+ cell selection from peripheral blood stem cells (PBSC) apheresis products, the CliniMACS and the Isolex 300i, were compared directly by pooling and splitting two PBSC harvests collected on sequential days from 10 patients and processing half of each pooled harvest on each device. The CliniMACS product had significantly higher median CD34+ purity (90%vs 78%; P = 0.004) and lower median T-cell content (0.06%vs 0.44%; P = 0.003) compared with the Isolex 300i product. The median CD34+ yields were similar (64% and 60% respectively). However, when the functional capacities of the products were compared, the median recovery of colony-forming units was significantly greater from the Isolex 300i product (48%vs 38%; P = 0.035), as was expansion of cells in either erythroid or granulocytic lineage-specific liquid culture (2.1-fold more erythroid and 1.5-fold more granulocytic lineage progenitors on d 9 (P = 0.03 and 0.03 respectively). This was due to a higher proportion of apoptotic cells in the CliniMACS product (28%vs 18%; P = 0.007, annexin V binding). Hence, although the CliniMACS device yielded a higher purity product with fewer T cells, the Isolex 300i product contained fewer apoptotic cells and consequently had greater functional capacity in culture.