Large-scale commercial thinning of young forests in the Pacific Northwest is currently promoted on public lands to accelerate the development of late-seral forest structure for the benefit of wildlife species such as northern spotted owls (Strix occidentalis caurina) and their prey, including the northern flying squirrel (Glaucomys sabrinus). Attempts to measure the impact of commercial thinning on northern flying squirrels have mostly addressed short-term effects (2–5 years post-thinning) and the few published studies of longer-term results have been contradictory. We measured densities of northern flying squirrels 11–13 years after thinning of young (55–65 years) Douglas-fir forest stands in the Cascade Range of Oregon, as part of the Young Stand Thinning & Diversity Study. The study includes four replicate blocks, each consisting of an unthinned control stand and one stand each of the following thinning treatments: Heavy Thin; Light Thin; and Light Thin with Gaps. Thinning decreased density of northern flying squirrels, and squirrel densities were significantly lower in heavily thinned stands than in more lightly thinned stands. Regression analysis revealed a strong positive relationship of flying squirrel density with density of large (>30 cm diameter) standing dead trees and a negative relationship with percent cover of low understory shrubs. Maintaining sufficient area and connectivity of dense, closed canopy forest is recommended as a strategy to assure that long-term goals of promoting late-seral structure do not conflict with short-term habitat requirements of this important species.