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This retrospective study examined the differences in the prognostic impact of the haematopoietic cell transplantation-specific comorbidity index (HCT-CI) on transplant outcomes by disease status and time from transplant in allogeneic haematopoietic stem cell transplantation (HSCT) recipients at a Japanese transplant centre. Of 187 patients, nonrelapse mortality (NRM) at 3 years was 9.6, 21.2 and 27.8% in the low-risk (score 0), intermediate-risk (score 1–2) and high-risk (score 3) HCT-CI groups, respectively (P=0.03). The corresponding overall survival (OS) at 3 years was 70.1, 60.5 and 38.9%, respectively (P<0.01). In multivariate analyses, high-risk HCT-CI significantly predicted higher NRM (relative risk, (RR) 2.44 (95% confidence interval, (CI) 1.02–5.85); P=0.04) and worse OS (RR 2.02 (95% CI 1.15–3.54); P=0.01). In the subgroup analysis according to disease status, the HCT-CI was associated with OS (P<0.01) and NRM (P=0.07) in patients with low-risk diseases, but not in those with high-risk diseases. Within patients who survived without relapse >1 year after HSCT, the HCT-CI did not predict OS (P=0.59) or NRM (P=0.31). These findings can be useful to determine the role of pretransplant comorbidity in allogeneic HSCT. [ABSTRACT FROM AUTHOR]