FOXP3 has been proposed to be critical for the regulatory function of CD4(+)CD25+ T cells and it has been reported that its expression correlates with protection from graft-versus-host-disease (GvHD) after allogeneic hematopoietic stem cell transplantation (HSCT). Here, by monitoring 28 pediatric HSCT recipients, we found that the levels of FOXP3-mRNA expression in highly enriched CD4(+)CD25+ cells were identical to those in healthy controls irrespective of GvHD status. Moreover, FOXP3-mRNA was abundant in recently in vitro stimulated CD4(+)CD25+ cells that lacked regulatory function. Together these findings suggest that FOXP3-mRNA expression primarily reflects CD4(+)CD25+ cell frequency rather than defining the regulatory potential of CD4(+)CD25+ T cells and GvHD risk after HSCT.