Despite improvements in preventive and therapeutic strategies, acute graft-versus-host disease (aGvHD) remains a frequent complication of allogeneic hematopoietic stem cell transplantation (allo-HSCT). One attempt to prevent the development of aGvHD is the use of gut decontamination, ie, eliminating the patient’s intestinal microbiota by administering non-absorbable oral antibiotics. This approach was encouraged by murine studies in the 1970’s which found that resident intestinal bacteria played a role in the pathogenesis of aGvHD and that eradicating these bacteria prevented severe aGvHD [1]. Subsequent cohort studies published in the 1990’s reported that complete or more broad-spectrum gut decontamination lowered the incidence of aGvHD in both adult and paediatric patients undergoing allo-HSCT [2–5], leading to a wide practice of gut decontamination. However, since all studies were single-centre studies without a control group, later guidelines recommended that gut decontamination should generally not be offered [6]. Despite this, an informal survey of US transplant centres in a paper published last year [1] revealed that many still practice gut decontamination. To examine the effect of gut decontamination on the development of aGvHD in patients transplanted in more recent years, we undertook a retrospective cohort study of all patients who underwent their first allo-HSCT at Rigshospitalet in Copenhagen, Denmark in the period from 1998–2007. This cohort represents 148 patients transplanted before September 2002 who received gut decontamination with 5.4 g cefuroxime, 540mg tobramycin and 492mg nystatin, given daily from 7 days before stem cell infusion (day-7) until engraftment, and 135 patients transplanted after September 2002 when we made a policy decision to withhold all gut decontamination. At this time, we initiated prophylactic iv ceftazidime during neutropenia instead of using empiric iv piperacillin for neutropenic fever. Routine preventive measures were also reduced from use of gloves and gowns to hand-washing only. All patients received myeloablative conditioning, and, as GvHD prophylaxis, oral cyclosporine 6.25 mg/kg twice daily from day-1 combined with short-course iv methotrexate on days 1 (15 mg/m2), 3, 6 and 11 (10 mg/m2). Cyclosporine was tapered to stop at day 180, unless GvHD was present. We studied the retrospective cohort from day 0 until day+ 100. The primary outcome was the development of aGvHD grade II-IV, defined and graded according to standard criteria [7], and secondary outcomes were the development of gut aGvHD stage II-IV and non-relapse mortality (NRM). Patient and transplantation characteristics of gut decontaminated and non-decontaminated patients were compared using chi-square test for categorical data and Wilcoxon rank-sum test for continuous data. Cumulative incidences of outcomes in gut decontaminated and nondecontaminated patients were compared using Gray’s test treating relapse and death as competing risks for aGvHD outcomes and relapse as competing risk for the NRM outcome. To estimate hazard ratios (HR) for the associations between gut decontamination and the primary and secondary outcomes, we employed multivariate Cox proportional hazard regression models, censoring subjects at day+ 100, relapse and death (not the latter when NRM was the outcome), with the following a priori-defined covariates: patient age at transplantation, stem cell source, female donor to male recipient, donor relation and HLA matching, use of total body irradiation and use of anti-thymocyte globulin. Formal tests based on scaled Schoenfeld residuals were used to test …