Mixed chimerism (MC) within CD4+ and CD8+ T cell days 7 and 10 after allogeneic stem cell transplantation (SCT) was compared with the occurrence of acute graft-vs.-host disease (GVHD) in 34 patients after SCT. Acute GVHD was diagnosed in 22 patients within the first 3 months after SCT, 15 of these developed acute GVHD grades II-IV. The difference in the clearance rate of host T cell between the two days were compared. We found a significantly higher risk (p = 0.005) for developing acute GVHD grades II-IV in patients with complete donor CD4+ T-cell chimerism day 7 after SCT together with patients who increased 50% or more in donor CD4+ T cells between days 7 and 10 after SCT. Our data suggest that molecular monitoring of MC early after transplantation may be useful as a diagnostic tool in predicting the occurrence of moderate to severe acute GVHD after SCT.