Comorbidities affect clinical outcomes and costs in medicine. The hematopoietic cell transplantation (HCT)-specific comorbidity index (HCT-CI) predicts mortality risk after HCT. Its association with resource utilization (RU) is unknown. In this single-center, retrospective study, we examined the association of HCT-CI with RU (readmissions, length of hospital stay (LOS) and days out of hospital alive (DOHA)) in first 100 days (n = 328) and 1 year (n = 226) in allogeneic HCT patients from January 2010 to June 2014. Age, disease risk, conditioning and use of antithymocyte globulin were significantly different in the four groups with HCT-CI 0 to1 (n = 138), 2 (n = 56), 3 (n = 55) or ≥4 (n = 79). Although the readmissions were higher in the first 100 days for patients with HCT-CI >0–1 (P = 0.03), they were not significantly different in patients over 1 year (P = 0.13). In the multivariable analysis, patients with HCT-CI score of >0 to 1 had increased LOS and fewer DOHA in both 100 days and 1 year after HCT. In this exploratory analysis, we found that HCT-CI >0 to 1 is associated with increased RU after allogeneic HCT. Recognizing predictors of RU can identify patients at risk of high utilization and help understand what drives health-care costs.