We administered surveys to 100 chief executive officers (CEOs) of community health centers to determine their perceptions of the financial impact of the Health Disparities Collaboratives, a national quality improvement initiative. One third of the CEOs believed that the HDC had a negative financial impact on their health center, and this perception was significantly correlated with centers having a higher proportion of uninsured patients. Performance-based payment incentives may improve care but may also add new financial burdens to facilities that treat the uninsured population. As such, a provider's payer mix may need to be considered in the design of QI programs if they are to be sustainable.