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The spatial distribution of canopy trees in the temperate deciduous forests of the northeastern United States creates “neighborhoods” that vary in species composition as well as understory features. These neighborhoods may affect the distribution and abundance of generalist small-mammal seed predators by creating spatial variation in the availability of food resources, protective cover, and interactions with competitors. Small-mammal distribution and abundance may then influence tree population dynamics through variation in seed predation and seedling establishment. To determine if small-mammal activity patterns, seed survival, and seedling recruitment varied with neighborhood structure, we designed a study conducted at two habitat levels: canopy-tree neighborhoods, which reflected variation in seed production, and understory neighborhoods, which reflected differences in protective cover and interactions among animals. We live-trapped small mammals during the summer and fall of 1995 and 1996, experimentally measured seed survival in the falls of 1995 and 1996, and quantified total tree seedling recruitment in the spring of 1997. We developed a new method for nonlinear Poisson regression to relate canopy and understory neighborhood composition to small-mammal distribution and activity, seed survival, and seedling establishment. Small-mammal activity patterns changed between 1995 and 1996 in response to seed production. Canopy tree neighborhoods were a good predictor of overall small-mammal activity, and neighborhoods with high small-mammal activity had low seed survival. The canopy-tree neighborhoods with sufficient seed rain and high seed survival displayed increased seedling recruitment. Understory structure was a poor predictor of seed survival and seedling recruitment but appeared to be the primary axis along which habitat partitioning among mammal species took place when population densities were low. This study demonstrates that small-mammal seed predators influence tree recruitment patterns through their actions as seed predators in temperate deciduous forests, and that local effects of small mammals on seedling recruitment can be predicted from the species composition of tree neighborhoods.