Over 150,000 ha of standing forest was altered as a result of a large-scale blowdown in the Boundary Waters Canoe Area Wilderness, Minnesota in 1999. We collected data in summers 2000 and 2001 to assess the effects of windthrow perturbation on small mammal communities in northern coniferous forests. Small mammal diversity, as well as density of the two most common species, red-backed voles (Clethrionomys gapperi) and woodland jumping mice (Napaeozapus insignis), were determined in three different treatments with varying proportions of blowdown (<33%, 33–66% and >66% blowdown). Diversity of small mammals increased from 2000 to 2001 and was highest in forest stands with <33% blowdown. The density of the two most abundant species of small mammals also differed among blowdown categories. Red-backed voles predominated at all sites, but exhibited peak densities (>25 individuals/ha) at sites most affected by blowdown. In contrast, density of woodland jumping mice exhibited an inverse relationship with red-backed voles, attaining peak densities (8 individuals/ha) in stands with <33% blowdown. Age ratios (juveniles: adults) were not influenced by year for either woodland jumping mice or red-backed vole populations, but differed for vole populations among blowdown categories. Juvenile red-backed voles predominated at sites with 33–66% (2.2: 1) and <33% blowdown (1.2: 1). Red-backed voles selected for blowdown and appeared to displace other small mammal species from this habitat. Because red-backed voles feed on coniferous seedlings, are primary dispersers of mycorrhizae and are prey for many predators, their selection of blowdown habitat could significantly influence community assemblages and forest succession following blowdowns.