Sixty-one consecutive paediatric patients undergoing allogenic bone marrow transplantation (BMT) were screened prospectively for cytomegalovirus (CMV)-viraemia by PCR. Sixteen patients (26%) presented with single or recurrent CMV-viraemia between day -7 and + 100. Although only four of them had evidence of CMV-disease, there was a significant difference in the incidence of acute Graft versus Host Disease (GVHD) grade III-IV (75% vs 15.5%), liver-involvement (68% vs 13%) and the incidence of chronic GVHD (83% vs 13.8%) between CMV-PCR-positive and CMV-PCR-negative patients. Transplant-related mortality (TRM) was 43.7% in the CMV-PCR-positive group versus 13% in patients which had no evidence for CMV-viraemia. In all but one cases mortality in CMV-PCR positive patients was GVHD-associated. Pre-emptive therapy with gancyclovir in case of CMV-viraemia seemed to have no impact on incidence and severity of GVHD.