Twenty three allogeneic bone marrow transplant (BMT) patients with female donors and 23 female autologous transplant patients were assessed for clonality status after transplant to determine the nature of haemopoietic reconstitution. The X chromosome probes PGK, HPRT and M27 beta were used to assess clonality by analysis of X chromosome inactivation. Results were obtained for 15 allogeneic patients, 14 of whom gave polyclonal results after transplantation. One patient gave a skewed pattern of X chromosome inactivation after transplant due to extreme Lyonisation of the donor cells. Results were obtained from 19 autologous transplant patients, 17 of whom gave polyclonal results after transplant. Two patients gave patterns of skewed X chromosome inactivation in post-transplant samples, reflected in their constitutive DNA, due to extreme Lyonisation. The remaining patients could not be assessed because of hypermethylation of HpaII sites or indistinguishable digested and undigested alleles using M27 beta probe analysis. Haemopoietic reconstitution after allogeneic and autologous BMT, in our patients, was found to be polyclonal. Skewed patterns of X chromosome inactivation seen after transplant were due to extreme Lyonisation of the infused haemopoietic cells.