Forestry practices result in a range of levels of disturbance to forest ecosystems, from clearcutting and deferment (high disturbance) to single-tree selection cutting and unharvested forests (low disturbance). We investigated the effects of timber harvest and disturbance on small mammal species in the Allegheny Mountains of West Virginia. In 2003 and 2004, mammals were captured using Sherman box traps, individually marked, and released. We collected habitat data in 2004 to characterize macrohabitat at the stand level and microhabitat surrounding each trap. Trap success was significantly higher in disturbed habitats than undisturbed habitats for red-backed vole Myodes (Clethrionomys) gapperi (P  =  0.0012) and woodland jumping mouse Napaeozapus insignis (P  =  0.0221). Abundance estimated using the Jolly-Seber method was significantly higher in disturbed habitats for red-backed voles (P  =  0.0001). Adult northern short-tailed shrews Blarina brevicauda (P  =  0.0001) and white-footed and deer mice Peromyscus spp. (P  =  0.0254) weighed more in disturbed habitats. Small mammal distribution was strongly influenced by microhabitat factors, which differed substantially within stands. Leaf litter depth was a significant microhabitat factor for four of the five species analyzed, with red-backed voles (P  =  0.0001), woodland jumping mice (P  =  0.0001), Peromyscus spp. (P  =  0.0055), and eastern chipmunks Tamias striatus (P  =  0.0007) all preferring shallow leaf litter. These small mammal species responded neutrally or favorably to disturbance, and identified favorable microhabitat features regardless of stand type.