We prospectively evaluated mixed chimerism (MC) in the T cell and myeloid lineages and its correlation to busulphan, single-dose total body irradiation (TBI) and fractionated TBI (fTBI) conditioning in 180 patients with haematological malignancies after allogeneic stem cell transplantation (SCT). In all patients receiving busulphan, the area under curve (AUC) was calculated. The incidence of MC in the T cell lineage was significantly lower in patients receiving fTBI (22%) compared to those given TBI (53%, P=0.02) or busulphan (47%, P<0.01). The incidence of myeloid MC did not differ between the three groups. The overall probability of acute graft-versus-host disease grades II-IV was significantly higher in patients with complete T cell donor chimerism (49%) compared to patients with T cell MC (23%, P<0.001). The incidence of T cell and myeloid MC after SCT did not differ between low (55%), medium (42%) and high (43%) AUC levels of busulphan during conditioning. Patients receiving fTBI had a significantly higher probability of relapse compared to busulphan-treated patients (44 vs l6%, P=0.01). In multivariate analysis adjusted for diagnosis, busulphan-treated patients showed both a better survival (P=0.04) and less probability of relapse (0.03) compared to TBI-treated patients.