The real-world clinical and economic burden of graft-versus-host disease (GVHD) following allogeneic hematopoietic stem cell transplantation has not been comprehensively studied in France. Clinical outcomes, healthcare resource utilization and costs associated with acute GVHD (aGVHD), chronic GVHD (cGVHD), acute plus chronic GVHD (a+cGVHD) versus no GVHD were compared using French administrative claims data. After propensity score matching, 1934, 408, and 1268 matched pairs were retained for the aGVHD, cGVHD, and a+cGVHD cohorts, respectively. Compared with patients with no GVHD, odds of developing severe infection were greater in patients with aGVHD (odds ratio: 1.7 [95% confidence interval: 1.4, 2.1]). Compared with patients with no GVHD, mortality rates were higher in patients with aGVHD (rate ratio (RR): 1.6 [1.4, 1.7]) and with a+cGVHD (RR: 1.1 [1.0, 1.2]) but similar in patients with cGVHD (RR: 0.9 [0.7, 1.1]). Mean overnight hospital admission rates per patient-year were significantly higher in patients with aGVHD and a+cGVHD compared with no GVHD. Total direct costs (range €174,482–332,557) were 1.2, 1.5, and 1.9 times higher for patients with aGVHD, cGVHD, and a+cGVHD, respectively, versus patients with no GVHD. These results highlight the significant unmet need for effective treatments of patients who experience GVHD.