There are no cohort studies describing outcomes of patients colonized with vancomycin-resistant enterococci (VRE) undergoing allogeneic hematopoietic stem cell transplantation (AHSCT). We therefore conducted a retrospective cohort study of 217 consecutive adults undergoing AHSCT at the Mayo Clinic (Rochester, MN, USA) from 1998 to 2004. We analyzed the association between VRE colonization prior to transplant and 100-day post transplant mortality and morbidity. We identified 22 pretransplant VRE colonized patients and 195 non-colonized patients. Both groups had similar baseline characteristics with the following six exceptions. Colonized patients were more likely to have had pretransplant Clostridium difficile-associated diarrhea, pretransplant acute renal failure, AML, Cy/TBI conditioning, decreased platelet count at time of transplantation and myeloablative conditioning regimens. Overall, patients colonized with VRE were twice as likely to die by day 100 post transplant compared to non-colonized patients (hazard ratio: 2.1, P=0.028). This association persisted even after adjusting for differences in baseline characteristics. Increased mortality in the colonized group correlated with the presence of VRE bacteremia. Overall, pretransplant VRE colonization appears to be an independent risk factor for increased mortality post-AHSCT.