The enumeration of CD34+ cells by flow cytometry is commonly employed to assess progenitor/stem cell numbers in peripheral blood, cord blood, and apheresis products used for peripheral blood stem cell transplantation (PBSCT). Until recently, the enumeration of CD34+ cells has evolved in the absence of any procedural guidelines or quality assurance programs. We established a voluntary quality assurance for stem cell enumeration (QASE) program for Canadian laboratories involved in PBSCT. The goals of this study were 1) to survey current flow cytometric procedures for CD34 enumeration; 2) to evaluate inter-institutional reproducibility of currently employed assays; and 3) to evaluate the impact of adoption of a common method on inter-laboratory variability. Fourteen to nineteen laboratories participated in this program by enumerating CD34+ cells in shared cord blood samples. The survey showed a wide variation in flow cytometric methodology which in part contributed to the wide range in results obtained between different centres. Major differences in methodology included the number of events counted, use of isotype control and gating strategy. Participation in this program and adoption of a common methodology increased level of agreement for any given result although this trend did not reach statistical significance (P = 0.13). The results of this survey emphasize the need for a quality assurance program for stem cell enumeration by flow cytometry.