Interphase fluorescence in situ hybridization (FISH) for the translocation t(9;22) is widely used for quantifying minimal residual disease (MRD) in PBSC harvests from CML patients. We investigated the influence of cell composition on the percentage of positive FISH signals in 17 BCR/ABL-positive leukapheresis products from 12 CML patients. In these PBSC harvests, a significant correlation between the percentage of nonlymphocytic nucleated cells and BCR/ABL positivity was measured (k=0.81). This correlation was not seen in patients who became BCR/ABL negative after mini-ICE chemotherapy. CD34 enrichment was performed by immunomagnetic separation in 7 patients. There was a statistically significant increase in BCR/ABL positivity after CD34+ selection (p=0.018). This may have been caused by passive depletion of BCR/ABL-negative lymphocytes. Our findings suggest that quantitative results of t(9;22) FISH have to be corrected for cell composition when comparing different stem cell products. CD34+ selection before FISH analysis may be one way to enrich for nonlymphocytic cells and to concentrate on the progenitor compartment.