We prospectively monitored buffy coat leukocytes of 47 patients after 50 marrow transplantations (autologous n = 18, allogeneic n = 32) by polymerase chain reaction (PCR) for the presence of cytomegalovirus (CMV). None of the 18 autologous graft recipients (9 seropositive, 9 seronegative) had positive PCR results or CMV disease throughout the post-transplantation course. Six of 32 allograft recipients (19 seropositive, 13 seronegative) became PCR positive, four of whom developed CMV disease. PCR positive patients were found more often (5 of 10) in the group with acute GVHD grade II-IV compared with 1 of 22 in the group without or with grade I acute GVHD (p = 0.002). Comparison of PCR with antigen assay and virus culture showed an agreement in 90 of 96 (94%) samples. Discordant results were due to a higher sensitivity of the PCR compared with antigen assay (n = 4) and virus culture (n = 6). In conclusion, PCR helps to identify those patients who will not develop CMV disease and narrows down the number of patients who eventually will suffer symptomatic CMV infection. Furthermore, PCR is a useful tool for following the post-transplantation course with respect to CMV and for judging the effect of antiviral treatment.