Eastern spotted skunks (Spilogale putorius) have suffered a dramatic range-wide decline leading to concern that the species is likely vulnerable to extinction, but were recently discovered to persist in a portion of the southern Appalachian Mountains (United States). For 2 years we investigated habitat selection by eastern spotted skunks to develop an understanding of their habitat and conservation needs in northwestern South Carolina. We used a discrete choice modeling framework to evaluate vegetative and topographic features that we predicted would influence rest site selection by male and female spotted skunks. Using VHF telemetry, we tracked 15 spotted skunks (10 males and 5 females) to 215 day-time rest sites between the months of April and August. Spotted skunks selected rest sites in close proximity to drainage channels, where the relative probability of selection decreased 18% and 50% with every 20-m increase in distance to a drainage channel for males and females, respectively. Relative probability of selection by female spotted skunks increased 30% for every one-unit increase in coarse woody debris (CWD), and relative probability of selection by male spotted skunks increased 25% for every 10% increase in understory cover. These results are consistent with previous studies that have identified cover as important for protection from predators; however, we additionally identified CWD and drainage channels as important to habitat selection by spotted skunks. These latter attributes are likely selected based on prey availability, but alternate ecological functions of these features warrant further investigation. Preservation of understory vegetation and CWD within drainage networks might benefit conservation of eastern spotted skunks in the southern Appalachians.