Background: With healthcare cost in rise, it is of interest to explore variation in healthcare delivery outcome with different payment source. This study was aimed to analyze relationship between payment source and outcome following autologous hematopoietic stem cell transplant (AutoHSCT) in a national database. Methods: We identified all hospitalizations with AutoHSCT (n=1,673) from Nationwide Inpatient Sample (NIS), Healthcare Cost and Utilization Project (HCUP), Agency for Healthcare Research and Quality 2010 database using the ICD 9 procedure codes 41.04 and 41.07. Based on sample weights an estimated 8,444 AutoHSCT procedures were performed nationwide in 2010. Patients were stratified on the basis of payer status: Medicare (27%), Medicaid (12%), private insurance (60%), and uninsured (0.8%). Multivariable logistic regression models were used to determine the association of primary payer status and outcomes. Results: Patients had a mean age of 54 (±13) years, 39% were women and 69% were whites. In-hospital mortality occurred in 1.1%, 2.9% and 3.3% of AutoHSCT patients with primary payer status of private insurance, Medicaid and Medicare respectively. AutoHSCT patients with primary payer status of Medicaid and Medicare had a statistically significant higher chance of in-hospital mortality compared to patients with private insurance (adjusted odds ratios and 95% confidence intervals, 2.68; 1.54-4.65; P <0.001 and 1.90; 1.21-2.99; P=0.005 respectively). Length of stay was longer for Medicare patients (20 ± 11 days) and Medicaid patients (20 ± 12 days) compared to private insurance (18 ± 8 days; P <0.001). Medicare and Medicaid patients also accrued higher hospital charges (USD 175,221 and USD 166,453), compared to private insurance patients (USD 157,120; P <0.001). Conclusions: In this national study Medicaid and Medicare patients had an independent risk for in-hospital mortality compared to private insurance patients. Medicaid and Medicare patients also had longer length of hospital stays and accrued higher hospital charges. This may mandate a closer look into the current resource utilization strategies to reduce such disparities among patients undergoing AutoHSCT.