Cancer is a leading cause of death in the Appalachian region of the United States. Existing studies compare regional mortality rates to those of the entire nation. We compare cancer mortality rates in Appalachia to those of the nation, with additional comparisons of Appalachian and non-Appalachian counties within the 13 states that contain the Appalachian region. Lung/bronchus, colorectal, female breast and cervical cancers, as well as all cancers combined, are included in analysis. Linear regression is used to identify independent associations between ecological socioeconomic and demographic variables and county-level cancer mortality outcomes. There is a pattern of high cancer mortality rates in the 13 states containing Appalachia compared to the rest of the United States. Mortality rate differences exist between Appalachian and non-Appalachian counties within the 13 states, but these are not consistent. Lung cancer is a major problem in Appalachia; most Appalachian counties within the 13 states have significantly higher mortality rates than in-state, non-Appalachian counterparts. Mortality rates from all cancers combined also appear to be worse overall within Appalachia, but part of this disparity is likely driven by lung cancer. Education and income are generally associated with cancer mortality, but differences in the strength and direction of these associations exist depending on location and cancer type. Improving high school graduation rates in Appalachia could result in a meaningful long term reduction in lung cancer mortality. The relative importance of household income level to cancer outcomes may be greater outside the Appalachian regions within these states.