Cytomegalovirus (CMV) infection remains a major cause of morbidity and mortality in recipients of an allogeneic stem cell transplant (SCT). Due to the broad application of antiviral prophylaxis and preemptive therapy, a decrease in early-onset and a subsequent increase in late-onset CMV disease has been observed. New data on the latency state and reactivation of CMV have been presented, the role of T-cell responses in the control of CMV further substantiated, and viral immune escape mechanisms described in more detail. Sensitive diagnostic assays using nucleic acid amplification and hybridization techniques have been commercialized and will allow standardization of CMV diagnostics in antiviral drug trials. Quantification of the viral load will be increasingly considered for initiation and, in patients with persistence of high viral titers despite antiviral therapy, screening for antiviral drug resistance. Clinical data are emerging to show that, apart from ganciclovir, foscarnet can be given safely even after allogeneic SCT. Additional drugs like lobucavir and cidofovir have been used for specific indications. Interactions of immunosuppressive drugs and antiviral compounds of clinical relevance have been described. Thus, therapeutic drug monitoring and targeted antiviral drug dosing will become standard practice in antiviral treatment strategies in patients following allogeneic SCT.