The forests of the northeastern United States have become less contiguous and vigorous over the last century due to threats including acid rain, ice storm damage, and forest diseases. Often, trees have become the targets of widescale disease and pest out-breaks. Beech bark disease has been successful because of the effectiveness of the scale insect Cryptococcus fagisuga and the opportunistic Nectria coccinea var. faginata fungal vector. Since the severity of beech bark disease negatively affects mast production and canopy turnover, the abundance of small-mammal and insect populations can be limited. We explored the effects of beech bark disease, as well as other abiotic factors, on the diversity of small-mammal and invertebrate populations. We expected that biodiversity would vary according to disease severity in Fagus grandifolia (American Beech) stands, such that higher biodiversity and more seed predators would be noted in healthier forests. At sites in New York and Vermont, Sherman and pitfall traps were used to capture mammals and invertebrates, respectively. Correlations between tree size and disease severity levels were quantified by noting the diameter at breast height (dbh) and by ranking according to disease intensity levels. Although biodiversity indices were not significantly different among sites, there were significant differences in dbh (F = 3.48, P = 0.0154, d.f. = 3) and disease intensity levels (F = 21.13, P < 0.0001, d.f. = 3). Surprisingly in 2008, beechnut seed production was greatest in the Catskill Mountains of New York, the site with the greatest disease manifestation. Mammal richness was highest at the Champlain Valley site where there were fewer Napaeozapus insignius (Woodland Jumping Mice). Patterns of small-mammal abundance at the stand level, elucidated in canonical correspondence analyses, were explained in part by land-use history, soil characteristics, elevation, recent cutting, temperature, and precipitation in 2007. Invertebrate family richness was greatest in the Adirondacks of New York as compared to other sites. At the site level, beechnut density, land-use history, and soil order were the most important variables explaining variation in invertebrate assemblages. Results from this study show that patterns of biodiversity cannot be directly explained by disease and beech mast alone in the short-term. Rather, multi-year community dynamics must be measured.