Anthropogenic disturbance near rock outcrops occupied by Allegheny woodrats (Neotoma magister) is suspected of contributing to population declines in the northern and western peripheries of the species' distribution. We compared microhabitat characteristics among clearcut, diameter-limited and intact forest stands in the Allegheny mountains of West Virginia to determine effects of timber removal on Allegheny woodrat habitat selection. We measured microhabitat variables within 0.04-ha plots centered around foraging locations identified using radiotelemetry. Microhabitat variables also were measured in random plots within home ranges. We compared microhabitat variables among harvest methods, and between foraging and random plots within and across methods. Differences in microhabitats among timber harvest methods (F_{3, 14} = 20.31, P ≤ 0.001) were related to overstory characteristics, including total number of trees, canopy cover and overstory diversity. We observed no differences in microhabitat variables between foraging and random plots within any harvest method (F_{3, 82} = 1.20, P = 0.303). Differences between foraging and random plots across all methods (F_{1, 82} = 2.13, P = 0.036) related to understory diversity. Our results suggest that Allegheny woodrats tolerate a wide range of macrohabitat conditions, but habitat selection is primarily determined by microhabitat factors. Microhabitat selection may be related to the high mobility and generalist herbivore diet of this species.