Comorbidity is more common in older patients and can increase the cost of care by increasing toxicity. Using the SEER-Medicare database from 2000 to 2007, we examined the costs and life-year benefit of Auto-HSCT for MM patients over the age of 65 by evaluating the difference over time relative to comorbidity burden. One hundred ten patients had an Auto-HSCT in the early time period (2000-2003) and 160 in the late time period (2004-2007). Patients were divided by a Charlson Comorbidity Index (CCI) of 0 or greater than 1 (CCI1+). Median overall survival was 53.5 months for the late time period patients compared to 40.3 months for the early time period patients (p = 0.031). Median costs for CCI0 versus CCI1+ in the early period were, respectively, $70,900 versus $72,000 (100 d); $86,100 versus $98,300 (1 yr); and $139,200 versus $195,300 (3 yrs). Median costs for late period were, respectively, $58,400 versus $60,400 (100 d); $86,300 versus $77,700 (1 yr); and $124,400 versus $110,900 (3 yrs). Comorbidity had a significant impact on survival and cost among early time period patients but not among late time period patients. Therefore, older patients with some comorbidities can be considered for Auto-HSCT depending on clinical circumstances.