To characterize the costs of allogeneic hematopoietic cell transplantation with high-dose regimens (HDCT), we analyzed clinical information and costs of 315 HDCT recipients during a 4-year study period beginning in 2000. Multivariate analyses were performed to identify pre- and/or post-HDCT factors predicting higher costs within the first year. Overall survival (OS) at 100 days and 1 year were 80% and 58%, respectively. The median cost and days of hospitalization were $102,574 in 2004 US dollars and 36 days in the hospital for 100 days, and $128,800 and 39 days in the hospital for 1 year. Early costs, defined as costs within the first 100 days, accounted for 84% of total costs within the first year. Inpatient costs comprise 94% of the early costs, but only 61% of the later costs defined as costs incurred between 101 days and 1 year. Of the pre-HDCT factors, unrelated donors and advanced disease risk were significantly associated with increased cost. When post-HDCT events were also considered, these pre-HDCT factors were no longer independently predictive of high cost. Instead, severe complications post-HDCT were associated with higher costs, increasing total costs $20,228 on average. If no complications occurred, the mean cost within the first year was $79,222. These results provide cost estimates for complicated and uncomplicated HDCT procedures, as well as costs for management of specific transplant complications.