Recent reports indicate that human herpesvirus (HHV)-6 reactivation occurs in 40–50% of patients undergoing allogeneic stem cell transplantation (SCT). The risk factors that predispose to HHV-6 viremia are not well characterized. Available data suggest that that the frequency of reactivation is higher after allogeneic than after autologous stem cell transplantation. The clinical significance of HHV-6 reactivation, including its impact on engraftment, post-transplant complications, and overall outcome are not well understood. The aim of our study is to examine risk factors for HHV-6 reactivation following SCT and to characterize the clinical impact of this viral infection on stem cell transplant recipients. We report on 74 patients who underwent SCT between March 2003 and June 2004 (41 autologous and 33 allogeneic transplants) and who were tested for HHV-6 reactivation using a real-time quantitative PCR assay (Viracor, Lee’s Summit, MO, USA). A total of 242 samples (223 cell-free plasma samples, and 19 samples of other body fluids) were analyzed between 0 and 455 (median, 34) days after the transplant procedure. 41 samples from 25 patients were positive for HHV-6 DNA. Among them were 38 plasma samples with a median peak HHV-6 viral load of 2300 copies/ml (range, 100 – 830.500 copies/ml). HHV-6 DNA was detected in 28 of the 111 samples taken within 28 days after stem cell infusion, whereas only 13 of the 131 samples taken after the first 4 weeks tested positive (p = 0.003; Fisher’s exact test). Patients with HHV6 viremia had significantly longer hospital stays than those without detectable HHV-6 (median, 35 vs. 27 days, p = 0.011 by rank-sum test). Interestingly, this difference was limited to patients who had undergone autologous transplantation (median length of stay, 32.5 vs. 24 days, p = 0.008), whereas there was no difference in the length of hospital stay after allogeneic stem cell transplantation (median, 37.5 vs. 38.5 days, p = 0.81). HHV-6 viremia occurred with a similar frequency following autologous transplantation (12/41) as after allogeneic transplantation (13/33; p = 0.46, Fisher’s exact test). We also evaluated other possible risk factors for HHV-6 reactivation and found that age, sex, type of allotransplantation (related vs. unrelated donor), underlying disease, occurrence of graft-versus-host disease and use of T-cell antibodies in the conditioning regimen were not significantly associated with HHV-6 viremia. Moreover, there was no significant difference in the time to platelet or neutrophil engraftment between viremic patients and those without detectable HHV-6 DNA (median time to platelet engraftment, 20.5 vs. 18 days; median time to neutrophil engraftment, 17 vs. 15 days). Our data suggest that patients who undergo autologous SCT are at significant risk for HHV-6 reactivation, similar to those who receive allogeneic grafts. HHV-6 viremia occurs early during the post-transplant course, most often within the first 4 weeks. Recipients of autologous stem cell transplants with detectable plasma HHV-6 DNA levels have longer hospital stays than those without viremia, suggesting a more complicated post-transplant course. Whether HHV-6 reactivation by itself plays a causal role in delayed recovery or whether it is a reflection of the worse overall condition of these patients needs to be investigated further.