Wiskott-Aldrich syndrome (WAS) is caused by defects in the WAS protein (WASP) gene on the X chromosome. We previously reported that flow cytometric analysis of intracellular WASP expression (FCM-WASP) was useful in the diagnosis of WAS in patients and carriers. In this study, we applied FCM-WASP to evaluate the mixed chimera (MC) status of 12 WAS patients who underwent hematopoietic stem cell transplantation (HST). After HST, donor- and recipient-derived peripheral blood mononuclear cells (PBMCs) could be distinguished easily with this method, since the donor cells were WASP(bright), whereas the defective recipient cells were WASP(dim). Furthermore, with use of 2-color FCM-WASP, the MC status could be characterized by cell lineage. Six of the 12 patients with WAS were found to have MC status after HST, whereas others had complete chimera status. MC status was observed in every cell lineage examined. However, among PBMCs, recipient cells were most commonly observed in the monocyte population. Finally, to investigate the naive/memory status of donor and recipient T cells in these patients, 3-color FCM-WASP using anti-CD45RA or CD45RO was performed. We found that, in contrast to WASP(bright) T cells, most WASP(dim) T cells remained naive (CD45RA(+)/RO(-)) more than a year after HST. No imbalance in the ratio of naive to memory T cells was observed in WAS patients before HST. We conclude that FCM-WASP is a potentially useful method for clinical follow-up of WAS patients who have undergone HST. Our findings may also have important implications for the role of WASP during hematopoietic development.