Severe disturbance may alter or eliminate important habitat structure that helps preserve food caches of food-hoarding species. Recent recolonization of an insect-damaged forest by the endangered Mt. Graham red squirrel (Tamiasciurus hudsonicus grahamensis) provided an opportunity to examine habitat selection for midden (cache) sites following disturbance. From September 2003 to December 2005, we examined surface temperature and physical and vegetative characteristics associated with random locations and midden sites in insect-damaged forests. Red squirrel use of midden sites that are similar in structure to those used before insect infestation indicates that insect infestation did not eliminate midden habitat. However, differences between occupied middens and historical middens that are unoccupied reflect the severity of insect infestation tolerated by red squirrels. Occupied middens had <64% tree mortality, high basal area of live trees, and cooler surface temperatures during snow-free months. Forest areas with greater tree mortality would likely not represent habitat, threatening the persistence of an isolated population. Although conservation efforts can protect remaining habitat, disturbance events continually represent a threat. Habitat loss and predictions of increased disturbance due to climate change highlight the importance of documenting response to disturbance.