Exotic tree diseases have direct impacts on their host and may have indirect effects on native fauna that rely on host tree species. This paper reports on relative preference for European beech [Fagus sylvatica (L.)] and sugar maple [Acer saccharum (Marsh.)] seed to small mammals, the direct impacts of beech bark disease (BBD) on seed production of American beech [F. grandifolia (Ehrh.)], and indirect impacts of this disease complex on native small mammal fauna in the Upper Peninsula of Michigan. We expected these indirect effects to result from altered seed production in American beech, both in the short and long term. If present, a preference for beech could suggest a mechanism for an indirect impact of BBD on native small mammals. Seed production of infected American beech declined throughout the 3 y of the study, while production of trees in healthy stands varied annually. We found that the abundance of Peromyscus spp. were related to seed crop in the previous autumn but that the presence of the disease complex had no detectable effect on mouse populations. Variation in eastern chipmunk [Tamias striatus (L.)] population sizes were not explained by variation in seed production, although this species tended to be more abundant where beech was present. Finally, southern red-backed voles [Clethrionomys gapperi (Vigors)] were present in forests that did not contain American beech, apparently absent from forests with healthy beech, and present in low numbers in BBD-infected forests. We found that granivorous small mammals consistently preferred European beech seed over sugar maple seed. In general, our studies were indicative of limited short term impacts of BBD on small mammals but suggest the possibility of greater impacts in the future.