The Hematopoietic Cell Transplantation-specific Comorbidity Index (HCT-CI) is used to counsel patients regarding the risk of transplantation and selection of conditioning regimens. Pulmonary disease, most frequently demonstrated by a decreased diffusion capacity of carbon monoxide (DLCO), is the most prevalent comorbidity captured by the HCT-CI. The HCT-CI was validated using the Dinakara method for adjusting DLCO for Hb, but our institution and others utilize the Cotes method. The purpose of this study was to determine the impact of using the Cotes method rather than the Dinakara method on the HCT-CI score. We reviewed pre-transplant pulmonary function tests in 73 patients who underwent allogeneic hematopoietic SCT. Patients were stratified into low, intermediate or high-risk groups based on HCT-CI scores of 0, 1-2 or 3, respectively. We found that compared with the Dinakara method, the Cotes method increased the HCT-CI score in 45% of patients and resulted in total HCT-CI scores predictive of higher non-relapse mortality in 33% of patients. These results indicate that if an institution uses the Cotes method to adjust DLCO for Hb, their patients may be counseled to expect a higher risk of mortality than is actually predicted by the HCT-CI, and may be excluded from transplantation. Therefore, unless the HCT-CI is validated using other methods for correcting DLCO for Hb, the Dinakara method should be used.