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Summary. Serial samples were collected from 38 patients following allogeneic transplantation using either unmanipulated peripheral blood stem cells (PBSC) (n 18) or bone marrow (BM) (n 20) to assess the incidence of mixed chimaerism using PCR ampli®cation of ®ve VNTR regions. After ampli®cation, products were analysed using the Applied Biosystems ABI PRISM 377 Automated DNA Sequencer and GeneScan software GenoTyper program to determine a quantitative measure of chimaerism. The sensitivity of detection using this method was 0´1%.In the immediate post-transplant period (up to day 30) a signi®cantly lower incidence of mixed chimaerism (MC) occurred in recipients of PBSC compared to BM (P < 0´0005). Between 1 and 6 months there was a signi®cantly lower incidence of low-level MC in patients receiving PBSCT compared to BMT (4/14 v 8/11 respectively, P 0´04) in patients who had not rejected their grafts or relapsed. Similarly, beyond 6 months 0/9 PBSCT patients compared to 4/9 BMT patients showed MC (P 0´02). Beyond day 30 13/33 (39%) patients showed intermittent low-level MC, but this was not predictive for subsequent relapse. A rapidly increasing proportion of recipient haemopoiesis was predictive of graft rejection or relapse. Stable continuous MC without relapse was seen in one patient transplanted with PBSC for severe aplastic anaemia. These results suggest that the incidence of intermittent low-level MC is relatively high in the ®rst 6 months following unmanipulated haemopoietic stem cell transplantation but reduces with time and is signi®cantly lower in recipients of PBSC.