The association between dialysis facility size and mortality for patients undergoing hemodialysis remains largely unclear, and whether the relationship differs by race and ethnicity or among high-risk subgroups is not known. Using data from the USRDS, we analyzed mortality rates in 385,074 incident patients ages ≥ 18 years who received in-center hemodialysis at 4633 dialysis facilities between 2003 and 2009. Facilities were categorized by the number of hemodialysis stations (1-5, 6-10, 11-15, 16-20, 21-25, 26-30, 31-35, 36-45, 46-60, and ≥ 61 stations). We found significantly higher mortality associated with facilities comprising ≤ 15 stations, and within this group, mortality increased as the number of stations decreased. The association with increased mortality was weaker for facilities with 16-30 stations, but >30 stations offered no additional survival benefit. The association between increased mortality and facilities with ≤ 15 stations was stronger for racial minorities and patients with diabetes or cardiovascular diseases. After adjustments, blacks had a 78% greater 1-year mortality risk in facilities with one to five stations, whereas whites had only a 26% greater risk. Notably, other patient-related events remained comparable across the categories assessed. In summary, these data suggest that hemodialysis care at small facilities associates with a significant increase in mortality that is only partially explained by measured patient case mix, other well defined facility characteristics, and geographic region. Future studies should investigate differences in processes of care and practices among hemodialysis facilities of different sizes.