Chimaerism of FACS-sorted leucocyte subsets (CD14 þ , CD15 þ , CD3À/56 þ , CD3 þ /4 þ , CD3 þ /8 þ , CD19 þ ) was monitored prospectively between days þ 14 and þ 100 in 39 children undergoing allogeneic stem cell transplantation with reduced intensity-conditioning regimens. Cell subsets exceeding 1% of nucleated cells were subject to cell sorting. Chimaerism was analysed by dual-colour FISH and/or by short tandem repeat-polymerase chain reaction. The chimaerism pattern on day þ 28 was evaluated with regard to its correlation with graft rejection. Of 39 patients, nine patients had donor chimaerism (DC) in all subsets. Mixed/recipient chimaerism (MC/RC) was detectable within T cells in 62%, within NK cells in 39% and within monocytes and granulocytes in 38% of the patients. The correlation of secondary graft rejection with the chimaerism pattern on day þ 28 revealed the strongest association between RC in NK-cells (Po0.0001), followed by T cells (P ¼ 0.001), and granulocytes and monocytes (P ¼ 0.034). Notably, patients with RC in T cells rejected their graft only if MC or RC was also present in the NK-cell subset. By contrast, none of the children with DC in NK cells experienced a graft rejection. These observations suggest that, in the presence of recipient T-cell chimaerism, the chimaerism status in NK-cells on day þ 28 might be able to identify patients at high risk for late graft rejection.