Purpose of the study: No studies have compared the risk of mortality or graft-versus-host disease, in an inpatient setting in France, in allogeneic hematopoietic cell transplant recipients who develop cytomegalovirus disease with those who do not. This study assessed the impact of cytomegalovirus disease on clinical outcomes and healthcare resource utilization in allogeneic hematopoietic cell transplant recipients using the French Programme de Médicalisation des Systèmes d'Information database. Patients and methods: Recipients who had undergone allogeneic hematopoietic cell transplant in French hospitals between 2008 and 2011 were included in this retrospective, matched cohort study. Those with cytomegalovirus disease were each matched with two allogeneic hematopoietic cell transplant recipients without cytomegalovirus disease according to demographic and clinical characteristics. Probabilities of in-hospital mortality, graft rejection and/or graft-versus-host disease, and healthcare resource utilization were compared up to 12 months after cytomegalovirus disease diagnosis. Results: Overall, 4884 transplant recipients were enrolled, of which 194 had cytomegalovirus disease. Of these, 165 recipients with cytomegalovirus disease were matched to 330 without cytomegalovirus disease (1:2 ratio). The development of cytomegalovirus disease was associated with a significantly higher risk of in-hospital mortality (relative risk = 1.7, p = 0.0005) and higher cumulative number of inpatient days (p < 0.0001), but was not associated with a significantly higher risk of graft rejection and/or graft-versus-host disease or healthcare costs. Conclusions: Due to the increased risk of in-hospital mortality and higher cumulative number of inpatient days in allogeneic hematopoietic cell transplant recipients with cytomegalovirus disease versus those without, new strategies to prevent and manage cytomegalovirus disease are warranted.