The hair follicles of recipients of allogeneic hematopoietic SCT (HSCT) constitute the tissue with the greatest need for regeneration after high-dose chemotherapy. Previous studies have shown a lack of donor-derived DNA in the hair follicles of recipients. Therefore, we carried out a study to determine whether male donor-derived genetic material can be found in female recipients' hair follicles after HSCT. Fluorescent-based PCR with analyses of Y-chromosome STR (Y-STR) and RQ-PCR with the sex-determining region Y (SRY) were used independently to evaluate chimerism status. Our results proved the existence of donor-derived stem DNA in the recipients' hair follicle cells. This report undermines the validity of data indicating that hair follicle cells maintain 100% of recipient origin.