The aim of this retrospective study was to compare the efficacy and safety of standard intravenous ganciclovir (GCV) with low-dose oral valganciclovir (VGC) in preemptive treatment of cytomegalovirus (CMV) infection in patients who received allogeneic stem cell transplantation (ASCT). Fifty-nine adult ASCT patients with asymptomatic 68 CMV reactivations were included. For preemptive CMV treatment, VGC (900 mg/day) in 44 reactivations or GCV (5 mg/kg twice daily during the first week and once daily afterwards) in 24 CMV reactivations were administered for 21 days. Two consecutive negative results for PCR and/or CMV antigenemia were considered as treatment success. All patients with CMV reactivations were on immunosuppressive treatment. While no positivity was identified in any of the patients who received GCV on day 21, low-titer CMV positivity was noted in three of the patients in the VGC group (P = 0.264). In all three patients, VGC was continued at same dose and no positivity result was detected after 2-3 weeks. Low-grade neutropenia and high grade thrombocytopenia were significantly higher in the GCV group than in the VGC group (P = 0.018 and P = 0.04 respectively). Preemptive strategy of oral low-dose VGC appears preferable to the prevention of CMV disease in ASCT. These results require confirmation in prospective larger clinical studies.