Early diagnosis of CMV infection based on sensitive diagnostic assays has helped to reduce CMV-related mortality after allogeneic stem cell transplantation (SCT). In this study, the commercialized Murex CMV DNA Hybrid Capture assay (version 2.0) (HCS) was prospectively compared to an in-house CMV-DNA PCR assay from whole blood in patients after allogeneic stem cell transplantation. Overall, a high concordance between HCS and PCR was documented (kappa = 0.686; n = 385). The HCS assay was found to be as sensitive as the PCR indicating active CMV infection at a median of 35 and 34 days after transplantation, respectively. None of the HCS-negative patients developed CMV-related symptoms (negative predictive value 100%). Declining CMV DNA load in the blood was found to be an indicator for effective antiviral therapy, whereas persistence of a high viral load was associated with fatal CMV disease. In conclusion, the Hybrid Capture CMV DNA assay (v 2.0) allows early diagnosis of CMV infection after allogeneic SCT and assessment of the efficacy of antiviral therapy.