In chronic myeloid leukaemia, CD34+ stem/progenitor cells appear resistant to imatinib mesylate (IM) in vitro and in vivo. To investigate the underlying mechanism (s) of IM resistance, it is essential to quantify Bcr-Abl kinase status at the stem cell level. We developed a flow cytometry method to measure CrkL phosphorylation (P-CrkL) in samples with< 10 4 cells. The method was first validated in wild-type (K562) and mutant (BAF3) BCR-ABL+ as well as BCR-ABL−(HL60) cell lines. In response to increasing IM concentration, there was a linear reduction in P-CrkL, which was Bcr-Abl specific and correlated with known resistance. The results were comparable to those from Western blotting. The method also proved to be reproducible with small samples of normal and Ph+ CD34+ cells and was able to discriminate between Ph−, sensitive and resistant Ph+ cells. This assay should now enable investigators to unravel the mechanism (s) of IM resistance in stem cells.