We retrospectively evaluated the effect of 17 individual comorbidities, defined by the hematopoietic cell transplantation (HCT)‐specific comorbidity index, on non‐relapse mortality (NRM) and overall survival (OS) in 9531 patients aged between 16 and 70 years who underwent their first allogeneic HCT from 8/8 and 7/8 allele‐matched unrelated donors (8/8 and 7/8 MUDs) or single‐unit unrelated cord blood (UCB) between 2011 and 2020 using data from a Japanese registry database. In the multivariate analysis, infection (adjusted hazard ratio [HR], 1.62, 95% confidence interval [CI], 1.33–1.99 for 8/8 and 7/8 MUDs; adjusted HR, 1.33, 95%CI, 1.12–1.58 for UCB) and moderate/severe hepatic comorbidity (adjusted HR, 1.57, 95%CI, 1.04–2.38 for 8/8 and 7/8 MUDs; adjusted HR, 1.53, 95%CI, 1.09–2.15 for UCB) had a significant impact on NRM in both donor groups. Cardiac comorbidity (adjusted HR, 1.40, 95%CI, 1.08–1.80), mild hepatic comorbidity (adjusted HR, 1.22, 95%CI, 1.01–1.48), rheumatologic comorbidity (adjusted HR, 1.67, 95%CI, 1.11–2.51), renal comorbidity (adjusted HR, 2.44, 95%CI, 1.46–4.09), and severe pulmonary comorbidity (adjusted HR, 1.40, 95%CI, 1.11–1.77) were significantly associated with an increased risk of NRM but only in UCB recipients. Renal comorbidity had the strongest impact on poor OS in both donor groups (adjusted HR, 1.73, 95%CI, 1.10–2.72 for 8/8 and 7/8 MUDs; adjusted HR, 2.24, 95%CI, 1.54–3.24 for UCB). Therefore, unrelated donor selection should be taken into consideration along with the presence of specific comorbidities, such as cardiac, rheumatologic, renal, mild hepatic, and severe pulmonary comorbidities.