Background: Two CD34+ cell enumeration kits were recently introduced to offer a reproducible flow-cytometric quantification technique. We compared our in-house dual-platform CD34+ analysis procedure (standard method) with these two commercial single-platform kits. Methods: Cell samples comprising peripheral blood, apheresis products, and cord blood were prospectively analyzed with the standard method and with ProCOUNT(TM) (n = 143). 36 of the 143 specimens were also analyzed with Stem-Kit(TM). The bead-based ProCOUNT data were evaluated using the original 1.0.2 software (Pro-A) as well as the revised 2.0 version (Pro-B); the Stem-Kit results were based on beads (Stem-D) but also analyzed and calculated on leukocyte basis (Stem-C). Results: For absolute CD34+ cell enumeration, the mean bias (cells/mul) was 182 with method Pro-A (Wilcoxon's paired rank sum test, p < 0.0001), 88 with Pro-B (p = 0.428), 172 with Stem-C (p = 0.019), and 509 with Stem-D (p = 0.001). Only procedure B showed no significant difference to the in-house standard method. In terms of clinically relevant CD34+ cell numbers (>20/mul of peripheral blood), we observed a good agreement between the standard procedure and Pro-B (kappa = 0.8), and a fair agreement with Stem-D (kappa = 0.28). These results were also consistent when the samples were grouped by sample type. Conclusions: A very good agreement was observed between our standard technique and ProCOUNT 2.0 which provided reliable and rapid CD34+ values in all blood products tested. Our study underlines the importance of a validated in-house method as a quality control mechanism when introducing a new method for CD34+ cell enumeration.