The enactment of the Patient Protection and Affordable Care Act (ACA) has been expected to improve the coverage of health insurance, particularly as related to the coordination of seamless care and the continuity of elder care among Medicare beneficiaries. The analysis of longitudinal data (2007 through 2013) in rural areas offers a unique opportunity to examine trends and patterns of rural disparities in hospital readmissions within 30 days of discharge among Medicare beneficiaries served by rural health clinics (RHCs) in the eight southeastern states of the Department of Health & Human Services (DHHS) Region 4. The purpose of this study is twofold: first, to examine rural trends and patterns of hospital readmission rates by state and year (before and after the ACA enactment); and second, to investigate how contextual (county characteristic), organizational (clinic characteristic) and ecological (aggregate patient characteristic) factors may influence the variations in repeat hospitalizations. The unit of analysis is the RHC. We used administrative data compiled from multiple sources for the Centers of Medicare and Medicaid Services for a period of seven years. From 2007 to 2008, risk-adjusted readmission rates increased slightly among Medicare beneficiaries served by RHCs. However, the rate declined in 2009 through 2013. A generalized estimating equation of sixteen predictors was analyzed for the variability in risk-adjusted readmission rates. Nine predictors were statistically associated with the variability in risk-adjusted readmission rates of the RHCs pooled from 2007 through 2013 together. The declined rates were associated with by the ACA effect, Georgia, North Carolina, South Carolina, and the percentage of elderly population in a county where RHC is located. However, the increase of risk-adjusted rates was associated with the percentage of African Americans in a county, the percentage of dually eligible patients, the average age of patients, and the average clinical visits by African American patients. The sixteen predictors accounted for 21.52 % of the total variability in readmissions. This study contributes to the literature in health disparities research from the contextual, organizational and ecological perspectives in the analysis of longitudinal data. The synergism of multiple contextual, organizational and ecological factors, as shown in this study, should be considered in the design and implementation of intervention studies to address the problem of hospital readmissions through prevention and enhancement of disease management of rural Medicare beneficiaries.