Preexisting autoimmune disease affects 10-30% of patients with myelodysplastic syndromes (MDS). Studies comparing outcomes in MDS patients with and without autoimmune disease show discordant results. Using Surveillance, Epidemiology, and End Results (SEER)-Medicare, we conducted a population analysis to define the impact of autoimmunity on MDS outcomes. Cases were ascertained between 2007 - 2017 and claim algorithms employed to identify autoimmune disease, demographic characteristics, comorbidity scores, MDS histology, transfusion burden, treatment with hypomethylating agents and hematopoietic stem cell transplant. Cox regression models estimated the impact on survival and competing-risk regression models defined the effect on leukemic transformation. We analyzed 15,277 MDS patients, including 2,442 (16%) with preexisting autoimmune disease. The epidemiologic profile was distinctive in cases with preexisting autoimmunity, who were younger, predominantly female and had higher transfusion burden without difference in MDS histologic distribution. Autoimmune disease was associated with 11% decreased risk of death (hazard ratio [HR] 0.89, 95% confidence interval [CI], 0.85 - 0.94, p<0.001). The effect on risk of leukemic transformation differed based on MDS histology. In low-risk MDS histologies, autoimmunity was associated with a 1.9-fold increased risk of leukemia (HR 1.87, 95%CI, 1.17 - 2.99, p=0.008), while no significant effect was seen in other groups. These results suggest that autoimmune disease affects survival in MDS and is associated with decreased mortality. The survival effect was evident in low risk histologies despite higher risk of progression to leukemia. This could represent inflammation-driven hematopoiesis simultaneously favoring less aggressive phenotypes and clonal expansion, which warrants further investigation.