Preemptive treatment based on the sensitive detection of CMV-DNA has helped to reduce HCMV-related mortality after allogeneic stem cell transplantation (SCT). Detection of active viral replication might help to better predict HCMV disease. In this study, 33 recipients at risk for HCMV infection after allogeneic SCT were prospectively monitored 1x/week for active HCMV infection by NASBA, whole blood DNA-PCR and virus culture assays. Preemptive antiviral therapy was initiated after the second positive PCR result, while NASBA results were not considered for clinical decision-making. Overall, a high agreement between PCR and NASBA on a per sample (85.3%) and per patient (87.9%) level was demonstrated. HCMV DNA titers in the blood were found to be higher in PCR(+)/NASBA(+) compared to PCR(+)/NASBA(-) samples (P < 0.01). None of the NASBA-negative patients developed HCMV disease. Sixteen of 18 patients receiving PCR-based preemptive therapy were also found NASBA positive. There was no difference between the assays for the time to the first positive test result. However, the time to the first negative test result upon initiation of antiviral therapy was significantly shorter for the NASBA assay (P = 0.002), indicating a high positive predictive value to assess the efficacy of antiviral therapy. Three patients developed late-onset HCMV disease, all of whom were found to be PCR and NASBA positive. In conclusion, the data presented clearly demonstrate the value of patient monitoring using the NASBA assay to early diagnose active HCMV infection and to assess the efficacy of antiviral therapy in high risk patients after allogeneic SCT. A prospective comparison of PCR-based vs NASBA-based preemptive therapy is ongoing.