A new hematopoietic cell transplantation specific comorbidity index (HCT-CI), which was modeled to effectively capture comorbidity and predict post-transplant outcomes, has been evaluated in a cohort of patients with a variety of hematologic disorders. In this study, we applied the HCT-CI to 77 patients with severe aplastic anemia who underwent HCT at the Asan Medical Center, Seoul, Korea between February 1995 and September 2007. Pre-transplant HCT-CI score was calculated in each patient using the clinico-pathologic data, which were retrieved from Asan Medical Center Bone Marrow Transplantation Registry Database. HCT-CI score was 0 in 54 patients (70%), 1 in 16 (21%), 2 in four (5%), and 4 in one (1%). The most prevalent comorbidity captured by the HCT-CI was infection (n=11) followed by arrhythmia (n=6). During a median follow-up period of 54.4 months (range, 4.0 to 159.0 months), 19 patients died and 16 experienced primary or secondary graft failure. The 5-year probabilities of overall survival (OS) and event-free survival (EFS) were 73.4% and 63.3%, respectively. OS and EFS were significantly different according to HCT-CI score; OS 86.6% and EFS 74.3% in patients with score 0 versus 43.5% and 38.5% in those with score 1 or more (P<0.001 for OS and P=0.001 for EFS). Other significant prognostic factors for OS were age (<30 years vs. ≥30, 90.8% vs. 58.3%, P=.002), pre-transplant transfusion amount (<50 units vs. ≥50, 93.0% vs. 61.0%; P=.005) and time from diagnosis to HCT (<120 days vs. ≥120, 85.2% vs. 61.4%; P=.013), and prognostic factors for EFS were age (<30 years vs. ≥30, 81.0% vs. 48.4%, P=.003) and time from diagnosis to HCT (<120 days vs. ≥120, 77.4% vs. 48.3%; P=.007). Multivariate analysis after adjustment for other variables demonstrated that HCT-CI score (HR 10.022, P<.001 for OS; HR 4.644, P<.001 for EFS), age (HR 8.447, P=.002 for OS; HR 4.060, P=.003 for EFS), time from diagnosis to HCT (HR 5.783, P=.002 for OS; HR 3.956, P=.002 for EFS) were independently significant prognostic factors for both OS and EFS. In conclusion, our data indicate that the presence of pre-transplant comorbidity assessed by HCT-CI may predict worse outcomes after HCT in severe aplastic anemia.