In order to study the epidemiological characteristics of cytomegalovirus (CMV) infection in allogeneic hematopoietic stem cell transplantation (allo-HSCT) recipients by means of plasma real time quantitative polymerase chain reaction (RQ-PCR), 141 adult patients undergoing allo-HSCT between January 2008 and June 2010 were serially monitored by RQ-PCR for detecting CMV and guiding the preemptive therapy followed up to 180 days post-HSCT. The results showed that the incidence of CMV infection and CMV pneumonia was 81.5% and 2.9% respectively, which mainly occurred within 2 months post-HSCT. Single-therapy with ganciclovir (GCV) for 63 patients or foscarnet 6 patients was performed for preemptive therapy. The total efficacy was 87.8%, and the response patterns were different. CMV infection was more frequent in female patients (P = 0.044), and those with aGVHD (P = 0.043), using ATG or basiliximab in conditioning regimens (P = 0.049), as well as earlier in patients using ATG or basiliximab or those with aGVHD (P = 0.007; P = 0.000). The aGVHD, maximum load, positive times of CMV-DNA detection and therapy duration all correlated with the efficacy (P < 0.05). It is concluded that the incidence of CMV infection is still high after HSCT. Plasma RQ-PCR assay for CMV-DNA shows a strong correlation with the clinical outcome of CMV infection, which is useful and suitable for management of CMV infection in HSCT.