OBJECTIVES: Cytomegalovirus (CMV) disease is a complication that may occur in association with haematopoietic cell transplantation (HCT). This retrospective, matched cohort study assessed the burden of CMV disease in HCT recipients in England using the Hospital Episodes Statistics database. METHODS: The impact of CMV disease on mortality, graft-versus-host disease (GVHD), relapse-free survival and healthcare resources up to 12 months after CMV disease diagnosis was assessed in recipients who underwent an HCT between April 2011 and May 2016. Each HCT recipient with CMV disease was randomly matched with two HCT recipients without CMV disease. Matching criteria were age, gender, indication for transplantation, previously received anti-thymocyte globulin and/or total body irradiation. RESULTS: Overall, 4863 HCT recipients were recorded. CMV disease was recorded as a primary/secondary diagnosis in 312 HCT recipients (6.4%), and commonly occurred ≤3 months post-transplant (n=210, 67.3%). HCT recipients without CMV disease had a significantly greater probability of overall survival (79.0%) versus those with CMV disease (70.8%; p-log-rank=0.0125). The logistic regression model showed that CMV disease was significantly associated with greater risk of in-hospital mortality (hazard ratio 1.40, 95% confidence interval 1.04–1.89). Probability of GVHD post-transplant was not significantly different between HCT recipients with and without CMV disease (23.3% vs 23.0%, respectively; p-log-rank=0.88). Probability of relapse, conditional on survival, was 19% in those with CMV disease and 22% in those without (p-log-rank=0.30). Mean healthcare costs were significantly higher in HCT recipients with CMV disease (£24,476) compared with those without (£17,610; p=0.0001). Generalised linear models showed that CMV disease led to increases of 44%, 30% and 30% in total costs, cumulative in-patient days and number of hospital re-admissions, respectively. CONCLUSIONS: This study highlights the burden of CMV disease in HCT recipients with substantial increases observed in mortality and hospital resource use in England.