The aim of the present study was to understand the impact of changes in the food environment on county-level obesity prevalence in the Appalachian Region. We examined the food environment in 412 counties across the Appalachian Region using data from the Behavioral Risk Factor Surveillance System, the American Community Survey, and the Food Environment Atlas. We found there was an overall decrease of per capita food stores from 2007 to 2011 in this region. There was also a significant relationship between the decrease of grocery stores per capita from 2007 to 2011 and the increase of county-level obesity in 2012. Our findings may provide insights into regional obesity disparities and county-level health policy strategies in the Appalachian region