The hematopoietic cell transplantation-specific comorbidity index (HCT-CI) was developed at a single center to predict outcomes for allogeneic transplant recipients who have comorbidities. The HCT-CI has not been widely validated in unselected transplant recipients. We evaluated whether the HCT-CI and other readily available pre-transplant variables predicted NRM and OS at a Canadian transplant center. Using a prospective cohort design, we analyzed consecutive adult allogeneic HCT recipients. Of 187 patients, HCT-CI risk was low in 22 (12%), intermediate in 50 (27%), high in 104 (55%) and undetermined in 11 (6%). Two-year OS was 45% (95% CI: 24-64%), 55% (95% CI: 40-68%) and 42% (95% CI: 32-51%) in the low, intermediate and high-risk HCT-CI groups, respectively. Two-year NRM was 36% (95% CI: 17-56%), 26% (95% CI: 15-39%) and 30% (95% CI: 22-39%) in the low, intermediate and high-risk HCT-CI groups, respectively. In multivariate analysis, the HCT-CI failed to predict OS or NRM. However, KPS of <90% at HCT was a strong predictor of NRM. In conclusion, the HCT-CI was not associated with NRM or OS. In contrast, KPS was an independent indicator of survival. International multi-center studies are required before the HCT-CI is used in clinical practice.